<?php
/**
* extracting data from original specimen data provider, following ABCD2.05 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
*/
$Units = $dom->getElementsByTagName('Unit');

  foreach ($Units as $Unit) {

    $UnitID = $Unit->getElementsByTagName('UnitID');
    $SourceInstitutionCode = $Unit->getElementsByTagName('SourceInstitutionID');
    $SourceName = $Unit->getElementsByTagName('SourceID');

 //   echo "Unit ID: " . $UnitID->item(0)->nodeValue . "<br>";
 //   echo "Source Institution: " . $SourceInstitutionCode->item(0)->nodeValue . "<br>";
 //   echo "Source Collection: " . $SourceName->item(0)->nodeValue . "<br>";

    $sqlUnitID = addslashes(utf8_decode($UnitID->item(0)->nodeValue));
    $sqlSourceInstitutionCode = addslashes(utf8_decode($SourceInstitutionCode->item(0)->nodeValue));
    $sqlSourceName = addslashes(utf8_decode($SourceName->item(0)->nodeValue));

/*----------------------------GATHERING--------------------------------------------------------- */

$Gatherings = $Unit->getElementsByTagName('Gathering');

  foreach ($Gatherings as $Gathering) {
    $CollectionDate = $Gathering->getElementsByTagName('DateTime');
    $GatheringAgents = $Gathering->getElementsByTagName('Agents');
    $Locality = $Gathering->getElementsByTagName('LocalityText');
    $Country = $Gathering->getElementsByTagName('Country');
    $NamedArea = $Gathering->getElementsByTagName('NamedArea');  //if (empty($Country))
    $AreaName = $Gathering->getElementsByTagName('AreaName');    
    $NearNamedPlaces = $Gathering->getElementsByTagName('NearNamedPlaces');  //if (empty($Country))
    $Altitude = $Gathering->getElementsByTagName('Altitude');
    
    $Longitude = $Gathering->getElementsByTagName('LongitudeDecimal');
    $Latitude = $Gathering->getElementsByTagName('LatitudeDecimal');
    $SiteCoordinates = $Gathering->getElementsByTagName('SiteCoordinatesSets');  //if (empty($Longitude & Latitude))  

    foreach ($Altitude as $AltitudeDetail) {
    
    $AltitudeLowerValue = $AltitudeDetail->getElementsByTagName('LowerValue');
    $AltitudeUpperValue = $AltitudeDetail->getElementsByTagName('UpperValue');
    
    if(!empty($AltitudeLowerValue))
    {$sqlAltitude = $AltitudeLowerValue->item(0)->nodeValue;}
    if(!empty($AltitudeUpperValue))
    { $sqlAltitude .= $AltitudeUpperValue->item(0)->nodeValue;} 

    
    }
    
    foreach ($CollectionDate as $DateTime) {
    
    $CollectionDateText = $DateTime->getElementsByTagName('DateText');
    $GatheringISODateTimeBegin = $DateTime->getElementsByTagName('ISODateTimeBegin');
    $GatheringDayNumberBegin = $DateTime->getElementsByTagName('DayNumberBegin');
    $GatheringTimeOfDayBegin = $DateTime->getElementsByTagName('ISOTimeOfDayBegin');    
    $GatheringISODateTimeEnd = $DateTime->getElementsByTagName('ISODateTimeEnd');
    $GatheringDayNumberEnd = $DateTime->getElementsByTagName('DayNumberEnd');
    $GatheringTimeOfDayEnd = $DateTime->getElementsByTagName('TimeOfDayEnd');

    if(empty($CollectionDateText)) {
 //   echo "Date2: " . $CollectionDate->item(0)->nodeValue . "<br>";  //if (empty($CollectionDate))
    $sqlCollectionDate = addslashes($CollectionDate->item(0)->nodeValue); }
    else {
 //   echo "Date: " . $CollectionDateText->item(0)->nodeValue . "<br>";
    $sqlCollectionDate = addslashes($CollectionDateText->item(0)->nodeValue); }
    
    if($GatheringISODateTimeBegin) {
    $sqlCollectionDate .= " " . $GatheringISODateTimeBegin->item(0)->nodeValue; }
    
    if($GatheringDayNumberBegin) {
    $sqlCollectionDate .= " " . $GatheringDayNumberBegin->item(0)->nodeValue; }
    
    if($GatheringTimeOfDayBegin) {
    $sqlCollectionDate .= " " . $GatheringTimeOfDayBegin->item(0)->nodeValue; }
    
    if($GatheringISODateTimeEnd) {
    $sqlCollectionDate .= " " . $GatheringISODateTimeEnd->item(0)->nodeValue; }    
    
    if($GatheringDayNumberEnd) {
    $sqlCollectionDate .= " " . $GatheringDayNumberEnd->item(0)->nodeValue; }    
    
    if($GatheringTimeOfDayEnd) {
    $sqlCollectionDate .= " " . $GatheringTimeOfDayEnd->item(0)->nodeValue; }    

    }
    

    foreach ($GatheringAgents as $Collectors) {

      $PersonName = $Collectors->getElementsByTagName('GatheringAgent');
      $AgentText = $Collectors->getElementsByTagName('GatheringAgentsText');   //if (empty($Collectors)
      
      
      if(empty($PersonName->item(0)->nodeValue)) {
 //       echo "Person: " . $PersonName->item(0)->nodeValue . "<br>"; 
        $sqlPersonName = addslashes(utf8_decode($AgentText->item(0)->nodeValue)); 
         }
       else {
        $sqlPersonName = addslashes(utf8_decode($PersonName->item(0)->nodeValue)); }

       }
  

  //    echo "Locality: " . $Locality->item(0)->nodeValue . "<br>"; 
      $sqlLocality = addslashes(utf8_decode($Locality->item(0)->nodeValue));

    foreach ($Country as $Countries) {

      $CountryName = $Countries->getElementsByTagName('Name');
      $ISO2 = $Countries->getElementsByTagName('ISO3166Code');
      
      
      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);
        }
       
       $sqlNamedAreas = addslashes($AreaName->item(0)->nodeValue);
       
       if($sqlNamedAreas = 'Africa' or $sqlNamedAreas = 'Asia' or $sqlNamedAreas = 'Australia' or $sqlNamedAreas = 'Australia and Oceania' or $sqlNamedAreas = 'Europe' or $sqlNamedAreas = 'Middle America' or $sqlNamedAreas = 'South America' or $sqlNamedAreas = 'Middle America' or $sqlNamedAreas = 'Middle and South America' or $sqlNamedAreas = 'North America' or $sqlNamedAreas = ' Atlantic Ocean' or $sqlNamedAreas = 'Arctic Ocean' or $sqlNamedAreas = 'Indian Ocean' or $sqlNamedAreas = 'Pacific Ocean' or $sqlNamedAreas = 'Southern Ocean' or $sqlNamedAreas = 'Landlocked Sea')
      
      { $sqlContinentOrOcean = addslashes($AreaName->item(0)->nodeValue); }

        else {
        
 //       echo "NamedAreas: " . $NamedAreas->item(0)->nodeValue . "<br>";
        $sqlGatheringOther = addslashes($NamedArea->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;
      

  } //foreach $Gatherings

/*----------------------------IDENTIFICATIONS--------------------------------------------------------- */
  
  $Identifications = $Unit->getElementsByTagName('Identification');
  
  foreach ($Identifications as $IndexIdentification => $Identification) {     // more than one Identification possible
  
     $TaxaIdentified = $Identification->getElementsByTagName('TaxonIdentified');
     $Preferred = $Identification->getElementsByTagName('PreferredFlag');
  
    foreach ($TaxaIdentified as $TaxonIdentified) {
  
     $NameAuthorYearString = $TaxonIdentified->getElementsByTagName('FullScientificNameString');     // Name, Author, Year
     $HigherTaxa = $TaxonIdentified->getElementsByTagName('HigherTaxon');
     $ScientificNames = $TaxonIdentified->getElementsByTagName('ScientificName');

   //  echo "Name All: " . $NameAuthorYearString->item(0)->nodeValue . "<br>";
     $sqlNameAuthorYearString[] = addslashes(utf8_decode($NameAuthorYearString->item(0)->nodeValue));
   //  echo "Preferred: " . $Preferred->item(0)->nodeValue . "<br>";
     $sqlPreferredIdentificationFlag[] = $Preferred->item(0)->nodeValue;

      foreach ($HigherTaxa as $index => $HigherTaxon1) { // more than one HigherTaxon per Identification possible
       
         $HigherTaxon = $HigherTaxon1->getElementsByTagName('HigherTaxonName');
         $TaxonRank = $HigherTaxon1->getElementsByTagName('HigherTaxonRank');
       
   //      echo "Higher Taxon: " .$HigherTaxon->item(0)->nodeValue." (".$TaxonRank->item(0)->nodeValue.")<br>";
         $sqlHigherTaxon[] = $HigherTaxon->item(0)->nodeValue;
         $sqlHigherTaxonRank[]  = $TaxonRank->item(0)->nodeValue;

      } //foreach $HugherTaxa
    
     foreach ($ScientificNames as $ScientificName) {
    
   //  $ScientificNamesAtomized = $ScientificName->getElementsByTagName('NameAtomised');

//     foreach ($ScientificNamesAtomized as $ScientificNameAtomized) {
    
      $Bacteria = $ScientificName->getElementsByTagName('Bacterial');
      $Botany = $ScientificName->getElementsByTagName('Botanical');
      $Zoology = $ScientificName->getElementsByTagName('Zoological');   
      $Virology = $ScientificName->getElementsByTagName('Viral');         
      

      if($Bacteria) {

        foreach ($Bacteria as $Bacterical) {
      
         $GenusBac = $Bacterical->getElementsByTagName('GenusOrMonomial');
         $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('GenusOrMonomial');
          $FirstEpithet = $Botanical->getElementsByTagName('FirstEpithet');
          $SecondEpithet = $Botanical->getElementsByTagName('InfraspecificEpithet');
          $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('GenusOrMonomial');
          $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('GenusOrMonomial');
        
   //       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 $ScientificNames
    
  } //foreach $TaxaIdentified
  
  } //foreach $Identifications
  
/*----------------------------------------MULTI MEDIA OBJECTS -----------------------------*/
  $MultiMediaObjects = $Unit->getElementsByTagName('MultiMediaObject');

foreach ($MultiMediaObjects as $IndexMultiMediaObjects => $MultiMediaObject) {     // more than one Identification possible
  
     $FileURI = $MultiMediaObject->getElementsByTagName('FileURI');
     $ProductURI = $MultiMediaObject->getElementsByTagName('ProductURI');
     
     $sqlFileURI[] = $FileURI->item(0)->nodeValue;
     $sqlProductURI[] = $ProductURI->item(0)->nodeValue;
     
  }   // foreach $MultiMediaObjects
  
  $TypeDesignations = $Unit->get_elements_by_tagname('NomenclaturalTypeDesignation');
  
  foreach ($TypeDesignations as $TypeDesignation) {
  
  $TypeStatus = $TypeDesignation->get_elements_by_tagname('TypeStatus');
  $sqlTypeStatus = $TypeStatus[0]->get_content();
  
  }
  
} //foreach $Units



?>