<?php
/**
* extracting data from original specimen data provider, following ABCD1.2 format, using DOM
* <br/><br/>
* @author Gabriele Droege, DNA Bank Network <contact@dnabank-network.org>
* @version 2.0
* @package Input
* @copyright Copyright © 2011 DNA Bank Network http://www.dnabank-network.org<br>The contents of this file are subject to the Mozilla Public License Version 1.1
* @filesource
* @license http://www.mozilla.org/MPL/ MPL
*/
$Datasets = $dom->getElementsByTagName('DataSet');

foreach ($Datasets as $Dataset) {

  $SourceInstitutionCode = $Dataset->getElementsByTagName('SourceInstitutionCode');
  $SourceName = $Dataset->getElementsByTagName('SourceName');

 // echo "Source Institution: " . $SourceInstitutionCode->item(0)->nodeValue . "<br>";
 // echo "Source Collection: " . $SourceName->item(0)->nodeValue . "<br>"; 
  $sqlSourceInstitutionCode = addslashes($SourceInstitutionCode->item(0)->nodeValue);
  $sqlSourceName = addslashes($SourceName->item(0)->nodeValue);

$Units = $Dataset->getElementsByTagName('Unit');

foreach ($Units as $Unit) {

  $UnitID = $Unit->getElementsByTagName('UnitID');
  $GatheringNo = $Unit->getElementsByTagName('CollectorsFieldNumber');
  
 // echo "Unit ID: " . $UnitID->item(0)->nodeValue . "<br>";
  $sqlUnitID = addslashes($UnitID->item(0)->nodeValue);
  $sqlGatheringNo = addslashes($GatheringNo->item(0)->nodeValue);
  
/*----------------------------GATHERING---------------------------------------------------------*/
  
  $Gatherings = $Unit->getElementsByTagName('Gathering');

  foreach ($Gatherings as $Gathering) {

    $CollectionDate = $Gathering->getElementsByTagName('DateText');
    $GatheringDateText = $Gathering->getElementsByTagName('GatheringDateTime');  //if (empty($CollectionDate))
    $GatheringISODateTimeBegin = $Gathering->getElementsByTagName('ISODateTimeBegin');
    $GatheringDayNumberBegin = $Gathering->getElementsByTagName('DayNumberBegin');
    $GatheringTimeOfDayBegin = $Gathering->getElementsByTagName('ISOTimeOfDayBegin');    
    $GatheringISODateTimeEnd = $Gathering->getElementsByTagName('ISODateTimeEnd');
    $GatheringDayNumberEnd = $Gathering->getElementsByTagName('DayNumberEnd');
    $GatheringTimeOfDayEnd = $Gathering->getElementsByTagName('TimeOfDayEnd');
    $GatheringAgents = $Gathering->getElementsByTagName('GatheringAgent');
    $GatheringSites = $Gathering->getElementsByTagName('GatheringSite');
  

    if($GatheringDateText->item(0)->nodeValue != "") {
 //   echo "Date: " . $GatheringDateText->item(0)->nodeValue . "<br>";
    $sqlCollectionDate = addslashes($GatheringDateText->item(0)->nodeValue); }
    else { $sqlCollectionDate = ""; }
     
    if($GatheringISODateTimeBegin->item(0)->nodeValue != "") {
    $sqlCollectionDateMin = $GatheringISODateTimeBegin->item(0)->nodeValue; }
    
    if($GatheringDayNumberBegin->item(0)->nodeValue != "") {
    $sqlCollectionDateMin .= " " . $GatheringDayNumberBegin->item(0)->nodeValue; }
    
    if($GatheringTimeOfDayBegin->item(0)->nodeValue != "") {
    $sqlCollectionDateMin .= " " . $GatheringTimeOfDayBegin->item(0)->nodeValue; }
    
    if($GatheringISODateTimeEnd->item(0)->nodeValue != "") {
    $sqlCollectionDateMax = " " . $GatheringISODateTimeEnd->item(0)->nodeValue; }    
    
    if($GatheringDayNumberEnd->item(0)->nodeValue != "") {
    $sqlCollectionDateMax .= " " . $GatheringDayNumberEnd->item(0)->nodeValue; }    
    
    if($GatheringTimeOfDayEnd->item(0)->nodeValue != "") {
    $sqlCollectionDateMax .= " " . $GatheringTimeOfDayEnd->item(0)->nodeValue; }    
  
    foreach ($GatheringAgents as $Collectors) {

      $PersonName = $Collectors->getElementsByTagName('PersonName');
      $AgentText = $Collectors->getElementsByTagName('AgentText');   //if (empty($Collectors)
      
      if(empty($Collectors)) {
   //     echo "Person2: " . $AgentText->item(0)->nodeValue . "<br>";
        $sqlPersonName = addslashes($AgentText->item(0)->nodeValue); }

      else {
  //      echo "Person: " . $PersonName->item(0)->nodeValue . "<br>"; 
        $sqlPersonName = addslashes($PersonName->item(0)->nodeValue); } }
  
    foreach ($GatheringSites as $GatheringSite) {
  
      $Locality = $GatheringSite->getElementsByTagName('LocalityText');
      $ContinentOrOcean = $GatheringSite->getElementsByTagName('ContinentOrOcean');
      $CountryName = $GatheringSite->getElementsByTagName('CountryName');
      $Country = $GatheringSite->getElementsByTagName('Country');  //if (empty($CountryName))
      $ISO2 = $GatheringSite->getElementsByTagName('ISO2Letter');
      $NamedArea = $GatheringSite->getElementsByTagName('NamedArea');  //if (empty($Country))
      $NearNamedPlaces = $GatheringSite->getElementsByTagName('NearNamedPlaces');  //if (empty($Country))
      $Longitude = $GatheringSite->getElementsByTagName('LongitudeDecimal');
      $Latitude = $GatheringSite->getElementsByTagName('LatitudeDecimal');
      $SiteCoordinates = $GatheringSite->getElementsByTagName('SiteCoordinates');  //if (empty($Longitude & Latitude))  
      $Altitude = $GatheringSite->getElementsByTagName('Altitude');
  
  //    echo "Locality: " . $Locality->item(0)->nodeValue . "<br>"; 
      $sqlLocality = addslashes($Locality->item(0)->nodeValue);
  //    echo "Continent: " . $ContinentOrOcean->item(0)->nodeValue . "<br>"; 
      $sqlContinentOrOcean = addslashes($ContinentOrOcean->item(0)->nodeValue);
      

      if(empty($CountryName)) {
  //      echo "Country2: " . $Country->item(0)->nodeValue . "<br>"; 
        $sqlCountryName = addslashes($Country->item(0)->nodeValue); }
        
      else {
 //       echo "Country: " . $CountryName->item(0)->nodeValue . "<br>";
        $sqlCountryName = addslashes($CountryName->item(0)->nodeValue); }
      
  //      echo "ISO2: " . $ISO2->item(0)->nodeValue . "<br>";
        $sqlISO2 = addslashes($ISO2->item(0)->nodeValue);
      
      if(empty($NamedArea)) {
  //      echo "NearNamedPlaces: " . $NearNamedPlaces->item(0)->nodeValue . "<br>";
        $sqlGatheringOther = addslashes($NearNamedPlaces->item(0)->nodeValue);
        }
        
        else {
       if(!empty($GatheringOther)) {
 //       echo "NamedAreas: " . $NamedAreas->item(0)->nodeValue . "<br>";
        $sqlGatheringOther = addslashes($NamedAreas->item(0)->nodeValue);
        }      }
      
  //    echo "Longitude: " . $Longitude->item(0)->nodeValue . "<br>";
      $sqlLongitude = $Longitude->item(0)->nodeValue;
 //     echo "Latitude: " . $Latitude->item(0)->nodeValue . "<br>";
      $sqlLatitude = $Latitude->item(0)->nodeValue;
 //     echo "Coordinates: " . $SiteCoordinates->item(0)->nodeValue . "<br>";
  //    echo "Altitude: " . $Altitude->item(0)->nodeValue . "<br>";
      $sqlAltitude = addslashes($Altitude->item(0)->nodeValue);
    } // foreach $GatheringSites
  } //foreach $Gatherings

  
/*----------------------------IDENTIFICATIONS---------------------------------------------------------*/  
  
  $Identifications = $Unit->getElementsByTagName('Identification');
  
  foreach ($Identifications as $IndexIdentification => $Identification) {     // more than one Identification possible
  
//     $TaxaIdentified = $Identification->getElementsByTagName('TaxonIdentified');
  
   // foreach ($TaxaIdentified as $TaxonIdentified) {
  
     $NameAuthorYearString = $Identification->getElementsByTagName('NameAuthorYearString');            // Name, Author, Year
     $ScientificNamesAtomized = $Identification->getElementsByTagName('ScientificNameAtomized');
     $HigherTaxa = $Identification->getElementsByTagname('HigherTaxon');     

//     echo "Name All: " . $NameAuthorYearString->item(0)->nodeValue . "<br>";
     $sqlNameAuthorYearString[] = addslashes($NameAuthorYearString->item(0)->nodeValue);
 //    echo "Preferred: " . $Identification->getAttribute('PreferredIdentificationFlag') . "<br>";
     $sqlPreferredIdentificationFlag[] = $Identification->getAttribute('PreferredIdentificationFlag');

      foreach ($HigherTaxa as $index => $HigherTaxon) { // more than one HigherTaxon per Identification possible
       
 //        echo "Higher Taxon: " .$HigherTaxon->nodeValue." (".$HigherTaxon->getAttribute('TaxonRank').")<br>";
         $sqlHigherTaxon[] = $HigherTaxon->nodeValue;
         $sqlHigherTaxonRank[]  = $HigherTaxon->getAttribute('TaxonRank');

      } //foreach $HugherTaxa
    
     foreach ($ScientificNamesAtomized as $ScientificNameAtomized) {
    
      $Bacteria = $ScientificNameAtomized->getElementsByTagName('Bacterial');
      $Botany = $ScientificNameAtomized->getElementsByTagName('Botanical');
      $Zoology = $ScientificNameAtomized->getElementsByTagName('Zoological');   
      $Virology = $ScientificNameAtomized->getElementsByTagName('Viral');         
      

      if($Bacteria) {

        foreach ($Bacteria as $Bacterical) {
      
         $GenusBac = $Bacterical->getElementsByTagName('Genus');
         $SubgenusBac = $Bacterical->getElementsByTagName('Subgenus');
         $SpeciesEpithetBac = $Bacterical->getElementsByTagName('SpeciesEpithet');
         $SubspeciesEpithetBac = $Bacterical->getElementsByTagName('SubspeciesEpithet');
        
  //       echo "Genus: " . $GenusBac->item(0)->nodeValue . "<br>";
         $sqlGenus[] = $GenusBac->item(0)->nodeValue;
 //        echo "Subgenus: " . $SubgenusBac->item(0)->nodeValue . "<br>";
         $sqlSubgenus[] = $SubgenusBac->item(0)->nodeValue;         
 //        echo "Spec.Epi: " . $SpeciesEpithetBac->item(0)->nodeValue . "<br>";
         $sqlFirstEpithet[] = $SpeciesEpithetBac->item(0)->nodeValue;                  
 //        echo "SspEpi: " . $SubspeciesEpithetBac->item(0)->nodeValue . "<br>";
         $sqlSecondEpithet[] = $SubspeciesEpithetBac->item(0)->nodeValue;
         if(empty($sqlGenus) and empty($sqlSubgenus) and empty($sqlFirstEpithet) and empty($sqlSubspecies))
         {              
 //        echo "Bacteria_All: " . $Bacteria->item(0)->nodeValue . "<br>"; //if (empty -> $GenusBac, $SubgenusBac, $SpeciesEpithetBac, $SubspeciesEpithetBac)      
         $sqlName_All[] = $Bacteria->item(0)->nodeValue;    }     

        } //foreach $Bacteria
      } //if($Bacteria)

      if($Botany) {
      
        foreach ($Botany as $Botanical) {
        
          $GenusBot = $Botanical->getElementsByTagName('Genus');
          $FirstEpithet = $Botanical->getElementsByTagName('FirstEpithet');
          $SecondEpithet = $Botanical->getElementsByTagName('SecondEpithet');
          $Rank = $Botanical->getElementsByTagName('Rank');
          $HybridFlag = $Botanical->getElementsByTagName('HybridFlag');
        
  //        echo "Genus: " . $GenusBot->item(0)->nodeValue . "<br>";
          $sqlGenus[] = $GenusBot->item(0)->nodeValue;         
 //         echo "Spec.Epi: " . $FirstEpithet->item(0)->nodeValue . "<br>";
          $sqlFirstEpithet[] = $FirstEpithet->item(0)->nodeValue;         
   //       echo "Rank: " . $Rank->item(0)->nodeValue . "<br>";            
          $sqlRank[] = $Rank->item(0)->nodeValue;                   
  //        echo "Sec.Epi: " . $SecondEpithet->item(0)->nodeValue . "<br>";    
          $sqlSecondEpithet[] = $SecondEpithet->item(0)->nodeValue;                   
  //        echo "Hybrid: " . $HybridFlag->item(0)->nodeValue . "<br>";
          $sqlHybridFlag[] = $HybridFlag->item(0)->nodeValue;           
          if(empty($sqlGenus) and empty($sqlFirstEpithet) and empty($sqlRank) and empty($sqlSecondEpithet))
          {        
  //        echo "Botany_All: " . $Botany->item(0)->nodeValue . "<br>"; //if (empty -> $GenusBot, $FirstEpithet, $SecondEpithet, $Rank, $HybridFlag)      
          $sqlName_All[] = $Botany->item(0)->nodeValue;   }
      
        } //foreach $Botany
      } //if($Botany)
      
      if($Zoology) {
      
        foreach ($Zoology as $Zoological => $Zoo) {
      
          $GenusZoo = $Zoo->getElementsByTagName('Genus');
          $SubgenusZoo = $Zoo->getElementsByTagName('Subgenus');
          $SpeciesEpithetZoo = $Zoo->getElementsByTagName('SpeciesEpithet');
          $SubspeciesEpithetZoo = $Zoo->getElementsByTagName('SubspeciesEpithet');

  //        echo "Genus: " .$GenusZoo->item(0)->nodeValue."<br>"; 
          $sqlGenus[] = $GenusZoo->item(0)->nodeValue;                   
 //         echo "Subgenus: " . $SubgenusZoo->item(0)->nodeValue . "<br>";
          $sqlSubgenus[] = $SubgenusZoo->item(0)->nodeValue;         
  //        echo "Spec.Epi: " . $SpeciesEpithetZoo->item(0)->nodeValue . "<br>"; 
          $sqlFirstEpithet[] = $SpeciesEpithetZoo->item(0)->nodeValue;                   
  //        echo "SspEpi: " . $SubspeciesEpithetZoo->item(0)->nodeValue . "<br>";
          $sqlSecondEpithet[] = $SubspeciesEpithetZoo->item(0)->nodeValue;
          if($sqlSecondEpithet) {
            $sqlRank = "ssp."; }
          if(empty($sqlGenus) and empty($sqlSubgenus) and empty($sqlFirstEpithet) and empty($sqlSecondEpithet))
            {        
   //         echo "Zoology_All: " . $Zoo->nodeValue . "<br>"; //if (empty -> $GenusZ, $SubgenusZ, $SpeciesEpithetZ, $SubspeciesEpithetZ)      
            $sqlName_All[] = $Zoology->item(0)->nodeValue; }
      
        } //foreach $Zoology
      } //if($Zoology)
      
      if($Virology)
      {
      
        foreach ($Virology as $Viral) {
        
          $GenusV = $Viral->getElementsByTagName('Genus');
        
    //      echo "Genus: " . $GenusV->item(0)->nodeValue . "<br>";
          $sqlGenus[] = $GenusV->item(0)->nodeValue;
          if(empty($sqlGenus)) 
          {              
 //         echo "Virology_All: " . $Virology->item(0)->nodeValue . "<br>";
          $sqlName_All[] = $Virology->item(0)->nodeValue; }
      
        } //foreach $Virology
      } //if($Virology)
    
    } //foreach $ScientificNamesAtomized
    
 // } //foreach $TaxaIdentified
  
  } //foreach $Identifications
  
/*----------------------------------------MULTI MEDIA OBJECTS -----------------------------*/
  $MultiMediaObjects = $Unit->getElementsByTagName('UnitDigitalImage');

foreach ($MultiMediaObjects as $IndexMultiMediaObjects => $MultiMediaObject) {     // more than one Identification possible
  
     $FileURI = $MultiMediaObject->getElementsByTagName('ImageURI');
     
     $sqlFileURI[] = $FileURI->item(0)->nodeValue;

     
  }   // foreach $MultiMediaObjects
  
  $TypeDesignations = $Unit->getElementsByTagName('NomenclaturalTypeDesignation');
  
  foreach ($TypeDesignations as $TypeDesignation) {
  
  $TypeStatus = $TypeDesignation->getElementsByTagName('TypeStatus');
  $sqlTypeStatus = $TypeStatus->item(0)->nodeValue;
  
  }
  
} //foreach $Units

} // foreach $Datasets


?>