<?
/**
 * Change Log:
 * 	Jul 14, 2023	Harman Singh	Migrated from PHP 5.3 to PHP 8.1
 */
#Transition: 			PHP 4.3 to PHP 5.16 to target PHP 5.3
#Testing environment: 	PHP 5.1.6
#Methods changed: 		modified getAll function - added $limit and $offset parameters
#Methods Tested: 		getAll & getById(104032)
#Testing Performed: 	Using pm3/test/manager_test_scripts/PcrManager_test.php
#DAO called: PcrDao
#DB directly called:  	NO
#Transition closed

class PcrManager {
	function __construct() {}

	/*************Modified By Lily*****************************/
	//function getAll() {
        /**
        * added the parameters $limit and $offset on Dec 20, 2010
        */
	function getAll($limit=false,$offset=false){
		$pcrDao= new PcrDao();
		//$result=$pcrDao->searchAll($limit,$offset);
		$result=$pcrDao->searchAll($limit,$offset);
		while ($row=pg_fetch_assoc($result)) {
			$pcr=new Pcr($row["id"]);
			$pcr->setSeqentry($row["fk_seqentry"]);
			$pcr->setPrimer_f($row["fk_primer_f"]);
			$pcr->setPrimer_r($row["fk_primer_r"]);
			$pcr->setNotes($row["note"]);
			$pcr->setUpdated($row["last_updated"]);
                        $pcr->setMarker( $row["fk_marker"]);
			$pcrlist[]=$pcr;
		}
		return $pcrlist;
	}
	/***********************************************/

	function getById($id) {
		$pcrDao= new PcrDao();
		$result=$pcrDao->searchByPcrid($id);
		while ($row=pg_fetch_assoc($result)) {
			$pcr=new Pcr($row["id"]);
			$pcr->setSeqentry($row["fk_seqentry"]);
			$pcr->setPrimer_f($row["fk_primer_f"]);
			$pcr->setPrimer_r($row["fk_primer_r"]);
			$pcr->setNotes($row["note"]);
			$pcr->setUpdated($row["last_updated"]);
                        $pcr->setMarker( $row["fk_marker"]);
		}
		return $pcr;
	}


	function getBySeqentry($seqid) {
		$pcrlist = NULL;
		$pcrDao= new PcrDao();
		$result=$pcrDao->searchBySeqentry($seqid);
		while ($row=pg_fetch_assoc($result)) {
			$pcr=new Pcr($row["id"]);
			$pcr->setSeqentry($row["fk_seqentry"]);
			$pcr->setPrimer_f($row["fk_primer_f"]);
			$pcr->setPrimer_r($row["fk_primer_r"]);
			$pcr->setNotes($row["note"]);
			$pcr->setUpdated($row["last_updated"]);
                        $pcr->setMarker( $row["fk_marker"]);
			$pcrlist[]=$pcr;
		}
		return $pcrlist;
	}

	function getBySeqentryMarker($seqid,$marker) {
		$pcrDao= new PcrDao();
		$result=$pcrDao->searchBySeqentryMarker($seqid,$marker);
		while ($row=pg_fetch_assoc($result)) {
			$pcr=new Pcr($row["id"]);
			$pcr->setSeqentry($row["fk_seqentry"]);
			$pcr->setPrimer_f($row["fk_primer_f"]);
			$pcr->setPrimer_r($row["fk_primer_r"]);
			$pcr->setNotes($row["note"]);
			$pcr->setUpdated($row["last_updated"]);
                        $pcr->setMarker( $row["fk_marker"]);
			$pcrlist[]=$pcr;
		}
		return $pcrlist;
	}

	function addPcr($pcr,$seqentryid) {
		$pcrDao= new PcrDao();
		if ($seqentryid) {
			if ( is_object($primer=$pcr->getPrimer_f()) ) $primer_f=$primer->getId();
			if ( is_object($primer=$pcr->getPrimer_r()) ) $primer_r=$primer->getId();

            $marker = $pcr->getMarker();
            if ( is_object($marker) )
                $markerID = $marker->getId();

			$result=$pcrDao->insertPcr($seqentryid,$primer_f,$primer_r, $markerID );

		} else $result=false;
		return $result;
	}

	function updatePcr($pcr) {
		$pcrDao= new PcrDao();
		if ($pcr->getSeqentry()) {
			if ( is_object($primer=$pcr->getPrimer_f()) ) $primer_f=$primer->getId();
			if ( is_object($primer=$pcr->getPrimer_r()) ) $primer_r=$primer->getId();

            $marker = $pcr->getMarker();
            if ( is_object($marker) )
                $markerID = $marker->getId();

			$result=$pcrDao->updatePcr($pcr->getId(),$pcr->getSeqentry(),$primer_f,$primer_r,$markerID);

		} else $result=false;
		return $result;
	}

	function deleteById($id){
		$pcrDao= new PcrDao();
		$result=$pcrDao->deleteById($id);
		return $result;
	}

}
?><?
/**
 * Change Log:
 * 	Jul 14, 2023	Harman Singh	Migrated from PHP 5.3 to PHP 8.1
 */
#Transition: PHP 4.3 to PHP 5.16 to target PHP 5.3
#Testing environment: 	PHP 5.1.6
#Methods changed: 		Modified getAll function
#Methods Tested: 		getAll & getById(4126830)
#Testing Performed: 	Using pm3/test/TraceWithsStatsManager_test.php
#DAO called: 			TraceWithStatsDao
#DB directly called:  	NO
#Transition closed
class TraceWithStatsManager {
	function __construct() {}

	/********************Modified By Lily********************************/
	//function getAll() {
	/* updated the parameters with $limit and $offset on Dec 20, 2010 */
	function getAll($offset=false,$limit=false) {
		$traceDao= new TraceWithStatsDao();
		//$result=$traceDao->searchAll();
		$result=$traceDao->searchAll($limit,$offset);
		while ($row=$pg_fetch_assoc($result)) {
			$trace=new TraceWithStats($row["id"]);
			$trace->setPCr($row["fk_pcr"]);
			$trace->setPrimer($row["fk_primer_seq"]);
			$trace->setRunsite($row["fk_site"]);
			$trace->setDirection($row["direction"]);
			$trace->setTracefile($row["trace_file"]);
			$trace->setPhredfile($row["phred_file"]);
			$trace->setTracename($row["tracename"]);
			$trace->setFormat($row["format"]);
			$trace->setSeqdate($row["seqdate"]);
			$trace->setStatus($row["status"]);
			$trace->setNotes($row["note"]);
			$trace->setUpdated($row["last_updated"]);
			$trace->setTamUri($row["tam_uri"]);
			$trace->setBases($row["bases"]);
			$trace->setMin($row["min"]);
			$trace->setMax($row["max"]);
			$trace->setMean($row["mean"]);
			$trace->setVar($row["var"]);
			$trace->setStdev($row["stdev"]);
			$trace->setSterr($row["sterr"]);
			$trace->setBin10($row["bin_10"]);
			$trace->setBin12($row["bin_12"]);
			$trace->setBin14($row["bin_14"]);
			$trace->setBin16($row["bin_16"]);
			$trace->setBin18($row["bin_18"]);
			$trace->setBin20($row["bin_20"]);
			$trace->setBin22($row["bin_22"]);
			$trace->setBin24($row["bin_24"]);
			$trace->setBin26($row["bin_26"]);
			$trace->setBin28($row["bin_28"]);
			$trace->setBin30($row["bin_30"]);
			$trace->setBin32($row["bin_32"]);
			$trace->setBin34($row["bin_34"]);
			$tracelist[]=$trace;
		}
		return $tracelist;
	}
	/*******************************************************/
	function getById($id) {

		$traceDao= new TraceWithStatsDao();
		$result=$traceDao->searchById($id);
		while ($row=$pg_fetch_assoc($result)) {
			$trace=new TraceWithStats($row["id"]);
			$trace->setPCr($row["fk_pcr"]);
			$trace->setPrimer($row["fk_primer_seq"]);
			$trace->setRunsite($row["fk_site"]);
			$trace->setDirection($row["direction"]);
			$trace->setTracefile($row["trace_file"]);
			$trace->setPhredfile($row["phred_file"]);
			$trace->setTracename($row["tracename"]);
			$trace->setFormat($row["format"]);
			$trace->setSeqdate($row["seqdate"]);
			$trace->setStatus($row["status"]);
			$trace->setNotes($row["note"]);
			$trace->setUpdated($row["last_updated"]);
			$trace->setTamUri($row["tam_uri"]);
			$trace->setBases($row["bases"]);
			$trace->setMin($row["min"]);
			$trace->setMax($row["max"]);
			$trace->setMean($row["mean"]);
			$trace->setVar($row["var"]);
			$trace->setStdev($row["stdev"]);
			$trace->setSterr($row["sterr"]);
			$trace->setBin10($row["bin_10"]);
			$trace->setBin12($row["bin_12"]);
			$trace->setBin14($row["bin_14"]);
			$trace->setBin16($row["bin_16"]);
			$trace->setBin18($row["bin_18"]);
			$trace->setBin20($row["bin_20"]);
			$trace->setBin22($row["bin_22"]);
			$trace->setBin24($row["bin_24"]);
			$trace->setBin26($row["bin_26"]);
			$trace->setBin28($row["bin_28"]);
			$trace->setBin30($row["bin_30"]);
			$trace->setBin32($row["bin_32"]);
			$trace->setBin34($row["bin_34"]);

		}
		return $trace;
	}


	function getByPcr($pcr) {
		$traceDao= new TraceWithStatsDao();
		$result=$traceDao->searchbyPcr($pcr);
		$tracelist = NULL;

		while ($row=$pg_fetch_assoc($result)) {
			$trace=new TraceWithStats($row["id"]);
			$trace->setPCr($row["fk_pcr"]);
			$trace->setPrimer($row["fk_primer_seq"]);
			$trace->setRunsite($row["fk_site"]);
			$trace->setDirection($row["direction"]);
			$trace->setTracefile($row["trace_file"]);
			$trace->setPhredfile($row["phred_file"]);
			$trace->setTracename($row["tracename"]);
			$trace->setFormat($row["format"]);
			$trace->setSeqdate($row["seqdate"]);
			$trace->setStatus($row["status"]);
			$trace->setNotes($row["note"]);
			$trace->setUpdated($row["last_updated"]);
			$trace->setTamUri($row["tam_uri"]);
			$trace->setBases($row["bases"]);
			$trace->setMin($row["min"]);
			$trace->setMax($row["max"]);
			$trace->setMean($row["mean"]);
			$trace->setVar($row["var"]);
			$trace->setStdev($row["stdev"]);
			$trace->setSterr($row["sterr"]);
			$trace->setBin10($row["bin_10"]);
			$trace->setBin12($row["bin_12"]);
			$trace->setBin14($row["bin_14"]);
			$trace->setBin16($row["bin_16"]);
			$trace->setBin18($row["bin_18"]);
			$trace->setBin20($row["bin_20"]);
			$trace->setBin22($row["bin_22"]);
			$trace->setBin24($row["bin_24"]);
			$trace->setBin26($row["bin_26"]);
			$trace->setBin28($row["bin_28"]);
			$trace->setBin30($row["bin_30"]);
			$trace->setBin32($row["bin_32"]);
			$trace->setBin34($row["bin_34"]);
			$tracelist[]=$trace;
		}
		return $tracelist;
	}

	function getByTracefile($tracefile) {
		$traceDao= new TraceWithStatsDao();
		$result=$traceDao->searchbyTraceFile($tracefile);
		if ($row=$pg_fetch_assoc($result)) {
			$trace=new TraceWithStats($row["id"]);
			$trace->setPcr($row["fk_pcr"]);
			$trace->setPrimer($row["fk_primer_seq"]);
			$trace->setRunsite($row["fk_site"]);
			$trace->setDirection($row["direction"]);
			$trace->setTracefile($row["trace_file"]);
			$trace->setPhredfile($row["phred_file"]);
			$trace->setTracename($row["tracename"]);
			$trace->setFormat($row["format"]);
			$trace->setSeqdate($row["seqdate"]);
			$trace->setStatus($row["status"]);
			$trace->setNotes($row["note"]);
			$trace->setUpdated($row["last_updated"]);
			$trace->setTamUri($row["tam_uri"]);
			$trace->setBases($row["bases"]);
			$trace->setMin($row["min"]);
			$trace->setMax($row["max"]);
			$trace->setMean($row["mean"]);
			$trace->setVar($row["var"]);
			$trace->setStdev($row["stdev"]);
			$trace->setSterr($row["sterr"]);
			$trace->setBin10($row["bin_10"]);
			$trace->setBin12($row["bin_12"]);
			$trace->setBin14($row["bin_14"]);
			$trace->setBin16($row["bin_16"]);
			$trace->setBin18($row["bin_18"]);
			$trace->setBin20($row["bin_20"]);
			$trace->setBin22($row["bin_22"]);
			$trace->setBin24($row["bin_24"]);
			$trace->setBin26($row["bin_26"]);
			$trace->setBin28($row["bin_28"]);
			$trace->setBin30($row["bin_30"]);
			$trace->setBin32($row["bin_32"]);
			$trace->setBin34($row["bin_34"]);
		}
		return $trace;
	}


}
?><?
/**
 * Change Log:
 * Jul 14, 2023	Harman Singh	Migrated from PHP 5.3 to PHP 8.1
 */
#Transition: PHP 4.3 to PHP 5.16 to target PHP 5.3
#Testing environment: 	PHP 5.1.6
#Methods changed: 		updated genDataObjs, getAllRaw and getAllAln methods
#Methods Tested: 		getAllRaw, getRawBySeqid(620), getAlnBySeqid(620)
#Testing Performed: 	test/manager_test_scripts/NucSeqManager_test.php
#DAO called: 			NucSeqDao
#DB directly called:  	NO
#Functions: 			- retrieve SeqData objects by seqid, marker, date and so on
#						- insert and update SeqData object
#Transition closed
class NucSeqManager {

	function genDataObjs($dbresult) {
		$objlist=false;
		if (pg_result_error($dbresult)) return FALSE; //changed from DB:: to PEAR::
		while ($row=pg_fetch_assoc($dbresult)) {
			$nucSeq=new CodingSeq($row["seqid"]);
			$nucSeq->setSeq(strtoupper($row["seq"]));
			$nucSeq->setLength($row["length"]);
			$nucSeq->setCds($row["cds"]);
			$nucSeq->setUpdated($row["updated"]);
			$nucSeq->setAmbiguous($row["ambiguous"]);
			$nucSeq->setMarker($row["fk_marker"]);

			$objlist[]= $nucSeq;
		}
		/* single object result */
		if (count($objlist)==1)
			return $objlist[0];
		/* multiple object result */
		else return $objlist;
	}

	/**
    * added the parameters $limit and $offset on Dec 21, 2010
    */
	function getAllRaw($limit=false,$offset=false) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAllRaw();
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getAll($limit,$offset);
		return NucSeqManager::generateRaw($seqDataArray);
	}

	/**
    * added the parameters $limit and $offset on Dec 21, 2010
    */
	function getAllAln($limit=false,$offset=false) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAllAln();
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getAll($limit,$offset);
		return NucSeqManager::generateAln($seqDataArray);
	}

	function getAllAlnCount() {
		/*$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAllRaw();
		$row=$result->fetchRow(MDB2_FETCHMODE_ASSOC);
		return $row["count"];*/

		return SeqDataManager::countAllNucAln();
	}

	function getRawBySeqid($seqid) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchRawBySeqid($seqid);
		return NucSeqManager::genDataObjs($result);*/

		$seqData=SeqDataManager::getBySeqId($seqid);
		if($seqData!=NULL)
			$raw=NucSeqManager::generateRaw($seqData);
		return $raw;
	}

	function getRawBySeqidArray($seqids) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchRawBySeqid($seqid);
		return NucSeqManager::genDataObjs($result);*/

		$seqData=SeqDataManager::getBySeqidArray($seqids);
		if($seqData!=NULL)
			$raw=NucSeqManager::generateRaw($seqData);
		return $raw;
	}


	function getRawBySeqidMarker($seqid,$marker) {
		//echo "getting : '$seqid'  '$marker'\n";
		$seqData=SeqDataManager::getBySeqIdMarker($seqid,$marker);
		if($seqData!=NULL)
			$raw=NucSeqManager::generateRaw($seqData);
		return $raw;
	}

	function getRawLengthBySeqidMarker($seqid,$marker) {
		$seqData = SeqDataManager::getLengthsBySeqIdMarker($seqid, $marker);
		if ( $seqData == NULL ) return NULL;
			return $seqData->getNucRawLength();
	}

	function getAlnLengthBySeqidMarker($seqid,$marker) {
		$seqData = SeqDataManager::getLengthsBySeqIdMarker($seqid, $marker);
		if ( $seqData == NULL ) return NULL;
			return $seqData->getNucAlnLength();
	}


	function getAlnBySeqid($seqid) {
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->searchAlnBySeqid($seqid);
		return NucSeqManager::genDataObjs($result);*/

		$seqData=SeqDataManager::getBySeqId($seqid);
		if($seqData!=NULL)
			$aln=NucSeqManager::generateAln($seqData);
		return $aln;
	}

	function getAlnBySeqidMarker($seqid,$marker) {

		$seqData=SeqDataManager::getBySeqidMarker($seqid,$marker);
		if($seqData!=NULL)
			$aln=NucSeqManager::generateAln($seqData);
		return $aln;
	}

	function saveRawSeq($seqObj,$site=NULL) {
		//$nucSeqDao= new NucSeqDao();
		$seqDataManager=new SeqDataManager();
		//$nucSeqDao->deleteRawBySeqidMarker($seqObj->getId(), $seqObj->getMarker());
		//$nucSeqDao->deleteAlnBySeqidMarker($seqObj->getId(), $seqObj->getMarker() );
		$seqObj->calcLength();
		/*$nucSeqDao->insertRaw(
			$seqObj->getId(),
			$seqObj->getSeq(),
			$seqObj->getLength(),
			$seqObj->getCds(),
			$seqObj->getAmbiguous(),
			$seqObj->getMarker()
		);*/
		//insert data into seqdata table
		$seqData=new SeqData();
		$seqData->setSeqId($seqObj->getId());
		$seqData->setMarker($seqObj->getMarker());
		$seqData->setNucRaw($seqObj->getSeq());
		$seqData->setNucRawLength($seqObj->getLength());
		$seqData->setNucRawCds($seqObj->getCds());
		$seqData->setSite($site);
		$seqDataManager->saveNucRaw($seqData);
	}

	function saveAlnSeq($seqObj) {
		//$nucSeqDao= new nucSeqDao();
		$seqDataManager=new SeqDataManager();

		/*$nucSeqDao->deleteAlnBySeqidMarker($seqObj->getId(), $seqObj->getMarker());
		$nucSeqDao->insertAln(
			$seqObj->getId(),
			$seqObj->getSeq(),
			$seqObj->getLength(),"NULL",
			$seqObj->getAmbiguous(),
			$seqObj->getMarker()
		);*/
		$seqData=new SeqData();
		$seqData->setSeqId($seqObj->getId());
		$seqData->setNucAln($seqObj->getSeq());
		$seqData->setNucAlnLength($seqObj->getLength());
		$seqData->setNucAlnCds($seqObj->getCds());

		$seqDataManager->saveNucAln($seqData);
	}

	//deprecated Jun 14, 2011 (no ambigoug count stored in DB table anymore)
	function updateAmbiguousNucaln($seqidarray){
		/*$nucSeqDao= new nucSeqDao();
		$nucSeqDao->updateAmbiguousAln($seqidarray);*/
	}

	function getAlnByDate($start=NULL,$end=NULL){
	/*	$nucSeqDao = new NucSeqDao();
		$result=$nucSeqDao->getAlnByDate($start,$end);
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDate($start,$end);
		return NucSeqManager::generateAln($seqDataArray);
	}

	function getAlnByDateMarker($start=NULL,$end=NULL,$marker){
	/*	$nucSeqDao = new NucSeqDao();
		$result=$nucSeqDao->getAlnByDate($start,$end);
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDateMarker($start,$end,$marker);
		return NucSeqManager::generateAln($seqDataArray);
	}

	function getRawByDate($start=NULL,$end=NULL){
	/*	$nucSeqDao= new NucSeqDao();
		$result=$nucSeqDao->getAlnByDate($start,$end);
		return NucSeqManager::genDataObjs($result);*/

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDate($start,$end);
		return NucSeqManager::generateRaw($seqDataArray);
	}

	function getRawByDateMarker($start=NULL,$end=NULL,$marker){

		$nucSeqArray=array();
		$seqDataArray=SeqDataManager::getByDateMarker($start,$end,$marker);
		return NucSeqManager::generateRaw($seqDataArray);
	}

	// FUNCTIONS FOR MULTIGENE TRANSITION
	function generateRaw($seqdataArray) {

		if ( !is_array ($seqdataArray) )
			$seqdataArray = array( $seqdataArray);

		foreach ( $seqdataArray as $seqdata )
		{
			$nucSeq=new CodingSeq($seqdata->getSeqId());
			$nucSeq->setSeq($seqdata->getNucRaw());
			$nucSeq->setLength($seqdata->getNucRawLength());
			$nucSeq->setCds($seqdata->getNucRawCds());
			$nucSeq->setUpdated($seqdata->getUpdate());
			$nucSeq->setAmbiguous($seqdata->getAmbiguous());
			$nucSeq->setMarker($seqdata->getMarker());
			$result[] = $nucSeq;
		}

		if ( count($result) == 1 )
			return $result[0];
		return $result;
	}

	function generateAln($seqdataArray) {
		if ( !is_array ($seqdataArray) )
			$seqdataArray = array( $seqdataArray);

		foreach ( $seqdataArray as $seqdata )
		{
			if ( count($seqdata->getNucAln()) == 0 )
				continue;
			$nucSeq=new CodingSeq($seqdata->getSeqId());
			$nucSeq->setSeq($seqdata->getNucAln());
			$nucSeq->setLength($seqdata->getNucRawLength());
			$nucSeq->setCds($seqdata->getNucAlnCds());
			$nucSeq->setUpdated($seqdata->getUpdate());
			$nucSeq->setAmbiguous($seqdata->getAmbiguous());
			$nucSeq->setMarker($seqdata->getMarker());
			$result[] = $nucSeq;
		}

		if ( count($result) == 1 )
			return $result[0];
		return $result;
	}
}


?><?
/**
 * 	Change Log:
 * 	Jul 18, 2023	Harman Singh	Migrated from PHP 5.3 to PHP 8.1
 */
#Transition: PHP 4.3 to PHP 5.16 to target PHP 5.3
#Testing environment: 	PHP 5.1.6
#Methods changed: 	None
#Methods Tested: 	getBySampleid
#Testing Performed: 	test/manager_test_scripts/FullRecordManager_test.php
#DAO called: 		MainRecordManager, SpecimendetailsManager, LocationManager, TaxonomyManager, GeoPolManager, PersonManager, and InstManager
#DB directly called:  	NO
#Functions: 		get FullRecord object by sampleid
#Transition closed

class FullRecordManager {

    function __construct() {

    }

    /**
     * This function get all the information of a record with the sample id as input.
     * @param string $sampleid
     * @return FullRecord object
     *
     */
    function getBySampleid($sampleid) {
	$fullrecord = new FullRecord();

	$record = MainRecordManager::getBySampleid($sampleid);
	$details = specimendetailsManager::getById($record->getSpecimenid());
	$location = LocationManager::getBySpecimenid($record->getSpecimenid());


	$fullrecord->setProcessid(trim($record->getProcessid()));
	$fullrecord->setSampleid(trim($record->getSampleid()));
	$fullrecord->setFieldnum(trim($record->getFieldnum()));
	$fullrecord->setCatalognum(trim($record->getCatalognum()));
	$fullrecord->setVoucher(trim($details->getVouchertype()));
	$fullrecord->setTaxid(trim($record->getTaxid()));
	$fullrecord->setName(trim($record->getTaxon()));

	switch ($record->getTaxonRank()) {
	    case 2: $fullrecord->setRank("phylum");
		break;
	    case 5: $fullrecord->setRank("class");
		break;
	    case 8: $fullrecord->setRank("order");
		break;
	    case 11: $fullrecord->setRank("family");
		break;
	    case 12: $fullrecord->setRank("subfamily");
		break;
	    case 14: $fullrecord->setRank("genus");
		break;
	    case 17: $fullrecord->setRank("species");
		break;
	}


	$fullrecord->setReproduction(trim($details->getReproduction()));
	$fullrecord->setSex(trim($details->getSex()));
	$fullrecord->setLifestage(trim($details->getLifestage()));
	$fullrecord->setCollectors(trim($details->getCollectors()));
	$fullrecord->setCollectiondate(trim($details->getCollectiondate()));
	$fullrecord->setLat(trim($location->getLat()));
	$fullrecord->setLon(trim($location->getLon()));
	$fullrecord->setCoordsource(trim($location->getSource()));
	$fullrecord->setRegion(trim($location->getRegion()));
	$fullrecord->setExactsite(trim($location->getSite()));

	$fullrecord->setLastupdated(trim($details->getLastUpdated()));

	if ($location) {
	    $geopolid = $location->getGeopol();
	    if ($geopolid) {
		$geopol = GeoPolManager::getById($geopolid);
		if ($geopol) {
		    if (strcmp($geopol->getRank(), "country") == 0) {
			$fullrecord->setCountry(trim($geopol->getName()));
		    } else {
			$fullrecord->setProvince(trim($geopol->getName()));
			$parent = GeoPolManager::getById($geopol->getParentid());
			$fullrecord->setCountry(trim($parent->getName()));
		    }
		}
	    }
	}

	if ($notesid = $details->getNotes()) {
	    $fullrecord->setNotes(trim(NotesManager::getById($notesid)));
	}

	if ($identifierid = $details->getIdentifier()) {
	    $person = PersonManager::getById($identifierid);
	    $fullrecord->setIdentifier(trim($person->getFullname()));
	}
	if ($instid = $record->getInst()) {
	    $inst = InstManager::getById($instid);
	    $fullrecord->setInst(trim($inst->getName()));
	}
	$fullrecords[] = $fullrecord;

	return $fullrecord;
    }

}

?><?
//chdir("/var/www/html/pm3");
//include "include/include.php";
/**
 * Change Log:
 * 	Jul 14, 2023	Harman Singh	Migrated from PHP 5.3 to PHP 8.1
 */
#Transition: PHP 4.3 to PHP 5.16 to target PHP 5.3
#Testing environment: 	PHP 5.1.6
#Methods changed: 		none
#Methods Tested: 		getAllPrefOptions, getOptionsByName (namesapce = "Project Console"), getPrefByUser (userid = "32").
#						Note: Userid is madeup.  Table not populated so expect no result for query.
#Testing Performed: 	test/test_UserPrefManager.php
#DAO called: 			UserPrefDao, UserPrefOptionsDao
#DB directly called:  	NO
#Functions: 			- getAllPrefOptions: retrieve all UserPref obj and add to a UserPrefSet obj
#						- allow get, update, insert, delete userPref
#Note					- can't do full testing.  Script still under developement.
#Transition closed

class UserPrefManager {

	//preference options
	function getAllPrefOptions($limit=NULL,$offset=NULL){
		$prefDao= new UserPrefOptionsDao();
		$result=$prefDao->searchAllOptions($limit,$offset);
		return UserPrefManager::processPrefOptionResults($result);
	}

	//preference options
	function  & getOptionsByName($namespace){
		$prefDao= new UserPrefOptionsDao();
		$result=$prefDao->searchOptionsByName($namespace);
		return UserPrefManager::processPrefOptionResults($result);
	}

	//preference options
	function processPrefOptionResults($result){
		if ( $result == NULL ||  pg_num_rows($result) < 1 )
			return false;
		$prefSet = new UserPrefSet();
		while ($row=$pg_fetch_assoc($result) ) {
			$pref = new UserPref();
			$pref->setId($row["id"]);
			$pref->setPredicate($row["predicate"]);
			$pref->setNamespace($row["namespace"]);
			$pref->setDescr($row["descr"]);
			$prefSet->addUserPref($pref);
		}
		return $prefSet;
	}

    //user preferences
	function getPrefByUser($userid){
		$prefDao= new UserPrefDao();
		$result=$prefDao->searchPrefByUser($userid);
		return UserPrefManager::processPrefResults($result);
	}

    //user preferences
	function processPrefResults($result){
		if ( $result == NULL ||  pg_num_rows($result) < 1 )
			return false;
		$prefSet = new UserPrefSet();

		while ($row=$pg_fetch_assoc($result) ) {
			$pref = new UserPref();
			$pref->setId($row["id"]);
			$pref->setPredicate($row["predicate"]);
			$pref->setNamespace($row["namespace"]);
			if ($row["pref_value"] == 't'){
				$pref->setPrefValue(true);
			}
			$prefSet->addUserPref($pref);
		}
		return $prefSet;
	}

	function insertUserPref($userid, $namespace, $predicate, $prefValue){
		$prefDao= new UserPrefDao();
		return $prefDao->insertUserPref($userid, $namespace, $predicate, $prefValue);
	}

	function updateUserPrefValue($userid, $namespace, $predicate, $prefValue){
		$prefDao= new UserPrefDao();
		return $prefDao->updateUserPrefValue($userid, $namespace, $predicate, $prefValue);
	}

	function updateUserPrefById($id, $userid, $namespace, $predicate, $prefValue){
		$prefDao= new UserPrefDao();
		return $prefDao->updateUserPrefById($id, $userid, $namespace, $predicate, $prefValue);
	}

	function deleteUserPrefById($id){
		$prefDao= new UserPrefDao();
		return $prefDao->deleteUserPrefById($id);
	}

	function addUserPrefByUserid($userid, $namespace, $predicate, $prefValue){
		$found=false;
		$prefSet=UserPrefManager::getPrefByUser($userid);
		if($prefSet){
			$prefArray=$prefSet->toArray();
			foreach($prefArray as $pref){
				if(!strcmp($pref->getNamespace(),$namespace) and !strcmp($pref->getPredicate(),$predicate)){
					$found=true;
					return UserPrefManager::updateUserPrefValue($userid, $namespace, $predicate, $prefValue);
					break;
				}
			}
		}

		if(!$found){
			return UserPrefManager::insertUserPref($userid, $namespace, $predicate, $prefValue);
		}

	}


}

//$pref = new UserPrefManager();
//$pref->insertUserPref(8,"Project List","Hide Public Projects",true);
//$pref->insertUserPref(8,"Project List","Hide Campaigns",false);
//$pref->updateUserPrefValue(8,"Project List","Hide Campaigns",true);
//$pref->updateUserPrefById(2,8,"Project List","Hide Campaigns Projects",false);
//$pref = $pref->getPrefByUser(8);
//$p = $pref->getAllPrefOptions();
//var_dump($p);
?>