<!-- Copyright (C) 2009 DNA Bank Network
http://www.dnabank-network.org

The contents of this file are subject to the Mozilla Public License Version 1.1
See LICENSE.TXT at the top of this package for the full license terms. -->


<?php

$dom = domxml_open_file($file);


$Units = $dom->get_elements_by_tagname('Unit');

  foreach ($Units as $Unit) {

    $UnitID = $Unit->get_elements_by_tagname('UnitID');
    $SourceInstitutionCode = $Unit->get_elements_by_tagname('SourceInstitutionID');
    $SourceName = $Unit->get_elements_by_tagname('SourceID');
    $GatheringNo = $Unit->get_elements_by_tagname('CollectorsFieldNumber');

 //   echo "Unit ID: " . $UnitID[0]->get_content() . "<br>";
 //   echo "Source Institution: " . $SourceInstitutionCode[0]->get_content() . "<br>";
 //   echo "Source Collection: " . $SourceName[0]->get_content() . "<br>";

    $sqlUnitID = addslashes(utf8_decode($UnitID[0]->get_content()));
    $sqlSourceInstitutionCode = addslashes(utf8_decode($SourceInstitutionCode[0]->get_content()));
    $sqlSourceName = addslashes(utf8_decode($SourceName[0]->get_content()));
    $sqlGatheringNo = addslashes(utf8_decode($GatheringNo[0]->get_content()));

/*----------------------------GATHERING--------------------------------------------------------- */

$Gatherings = $Unit->get_elements_by_tagname('Gathering');

  foreach ($Gatherings as $Gathering) {
    $GatheringDate = $Gathering->get_elements_by_tagname('DateTime');
    $GatheringAgents = $Gathering->get_elements_by_tagname('Agents');
    $LocalityText = $Gathering->get_elements_by_tagname('LocalityText');
    $Country = $Gathering->get_elements_by_tagname('Country');
    $NamedArea = $Gathering->get_elements_by_tagname('NamedArea');  //if (empty($Country))
    $AreaName = $Gathering->get_elements_by_tagname('AreaName');    
    $NearNamedPlaces = $Gathering->get_elements_by_tagname('NearNamedPlaces');  //if (empty($Country))
    $Altitude = $Gathering->get_elements_by_tagname('Altitude');
    
    $LongitudeDecimal = $Gathering->get_elements_by_tagname('LongitudeDecimal');
    $LatitudeDecimal = $Gathering->get_elements_by_tagname('LatitudeDecimal');
    $SiteCoordinates = $Gathering->get_elements_by_tagname('SiteCoordinatesSets');  //if (empty($LongitudeDecimal & LatitudeDecimal))  

    foreach ($Altitude as $AltitudeDetail) {
    
    $AltitudeLowerValue = $AltitudeDetail->get_elements_by_tagname('LowerValue');
    $AltitudeUpperValue = $AltitudeDetail->get_elements_by_tagname('UpperValue');
    
    if(!empty($AltitudeLowerValue))
    {$sqlAltitude = $AltitudeLowerValue[0]->get_content();}
    if(!empty($AltitudeUpperValue))
    { $sqlAltitude .= $AltitudeUpperValue[0]->get_content();} 

    
    }
    
    foreach ($GatheringDate as $DateTime) {
    
    $GatheringDateText = $DateTime->get_elements_by_tagname('DateText');
    $GatheringISODateTimeBegin = $DateTime->get_elements_by_tagname('ISODateTimeBegin');
    $GatheringDayNumberBegin = $DateTime->get_elements_by_tagname('DayNumberBegin');
    $GatheringTimeOfDayBegin = $DateTime->get_elements_by_tagname('ISOTimeOfDayBegin');    
    $GatheringISODateTimeEnd = $DateTime->get_elements_by_tagname('ISODateTimeEnd');
    $GatheringDayNumberEnd = $DateTime->get_elements_by_tagname('DayNumberEnd');
    $GatheringTimeOfDayEnd = $DateTime->get_elements_by_tagname('TimeOfDayEnd');

    if(empty($GatheringDateText)) {
    if($GatheringDate) {
 //   echo "Date2: " . $GatheringDate[0]->get_content() . "<br>";  //if (empty($GatheringDate))
    $sqlGatheringDate = addslashes($GatheringDate[0]->get_content()); }}
    else {
 //   echo "Date: " . $GatheringDateText[0]->get_content() . "<br>";
    $sqlGatheringDate = addslashes($GatheringDateText[0]->get_content()); }
    
    if($GatheringISODateTimeBegin) {
    $sqlGatheringDate .= " " . $GatheringISODateTimeBegin[0]->get_content(); }
    
    if($GatheringDayNumberBegin) {
    $sqlGatheringDate .= " " . $GatheringDayNumberBegin[0]->get_content(); }
    
    if($GatheringTimeOfDayBegin) {
    $sqlGatheringDate .= " " . $GatheringTimeOfDayBegin[0]->get_content(); }
    
    if($GatheringISODateTimeEnd) {
    $sqlGatheringDate .= " " . $GatheringISODateTimeEnd[0]->get_content(); }    
    
    if($GatheringDayNumberEnd) {
    $sqlGatheringDate .= " " . $GatheringDayNumberEnd[0]->get_content(); }    
    
    if($GatheringTimeOfDayEnd) {
    $sqlGatheringDate .= " " . $GatheringTimeOfDayEnd[0]->get_content(); }    

    }
    

    foreach ($GatheringAgents as $GatheringAgent) {

      $PersonName = $GatheringAgent->get_elements_by_tagname('GatheringAgent');
      $AgentText = $GatheringAgent->get_elements_by_tagname('GatheringAgentsText');   //if (empty($GatheringAgent)
      
      
      if(empty($PersonName)) {
        if($AgentText) {
 //       echo "Person: " . $PersonName[0]->get_content() . "<br>"; 
        $sqlPersonName = addslashes(utf8_decode($AgentText[0]->get_content())); }
         }
       else {
        $sqlPersonName = addslashes(utf8_decode($PersonName[0]->get_content())); }

       }
  
      if($LocalityText) {
  //    echo "Locality: " . $LocalityText[0]->get_content() . "<br>"; 
      $sqlLocalityText = addslashes(utf8_decode($LocalityText[0]->get_content())); }

    foreach ($Country as $Countries) {

      $CountryName = $Countries->get_elements_by_tagname('Name');
      $ISO2 = $Countries->get_elements_by_tagname('ISO3166Code');
      
      
      if(empty($CountryName)) {
          if($Country) {
 //       echo "Country2: " . $Country[0]->get_content() . "<br>"; 
        $sqlCountryName = addslashes($Country[0]->get_content()); } }
        
      else {
  //      echo "Country: " . $CountryName[0]->get_content() . "<br>";
        $sqlCountryName = addslashes($CountryName[0]->get_content()); }
      
        if($ISO2) {
 //       echo "ISO2: " . $ISO2[0]->get_content() . "<br>";
        $sqlISO2 = addslashes($ISO2[0]->get_content());  }}
      
      if(empty($NamedArea)) {
        if($NearNamedPlaces) {
  //      echo "NearNamedPlaces: " . $NearNamedPlaces[0]->get_content() . "<br>";
        $sqlGatheringOther = addslashes($NearNamedPlaces[0]->get_content());}
        }
       if($AreaName) {
       $sqlNamedAreas = addslashes($AreaName[0]->get_content()); }
       
       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[0]->get_content()); }

        else {
        if($NamedArea) {
 //       echo "NamedAreas: " . $NamedAreas[0]->get_content() . "<br>";
        $sqlGatheringOther = addslashes($NamedArea[0]->get_content()); }
        }      
        if($LongitudeDecimal) {
 //     echo "Longitude: " . $LongitudeDecimal[0]->get_content() . "<br>";
      $sqlLongitudeDecimal = $LongitudeDecimal[0]->get_content(); }
        if($LatitudeDecimal) {
  //    echo "Latitude: " . $LatitudeDecimal[0]->get_content() . "<br>";
      $sqlLatitudeDecimal = $LatitudeDecimal[0]->get_content(); }
      

  } //foreach $Gatherings

/*----------------------------IDENTIFICATIONS--------------------------------------------------------- */
  
  $Identifications = $Unit->get_elements_by_tagname('Identification');
  
  foreach ($Identifications as $IndexIdentification => $Identification) {     // more than one Identification possible
  
     $TaxaIdentified = $Identification->get_elements_by_tagname('TaxonIdentified');
     $Preferred = $Identification->get_elements_by_tagname('PreferredFlag');
  
    foreach ($TaxaIdentified as $TaxonIdentified) {
  
     $NameAuthorYearString = $TaxonIdentified->get_elements_by_tagname('FullScientificNameString');     // Name, Author, Year
     $HigherTaxa = $TaxonIdentified->get_elements_by_tagname('HigherTaxon');
     $ScientificNames = $TaxonIdentified->get_elements_by_tagname('ScientificName');

      if($NameAuthorYearString) {
   //  echo "Name All: " . $NameAuthorYearString[0]->get_content() . "<br>";
     $sqlNameAuthorYearString[] = addslashes(utf8_decode($NameAuthorYearString[0]->get_content())); }
     if($Preferred) {
   //  echo "Preferred: " . $Preferred[0]->get_content() . "<br>";
     $sqlPreferredIdentificationFlag[] = $Preferred[0]->get_content(); }

      foreach ($HigherTaxa as $index => $HigherTaxon1) { // more than one HigherTaxon per Identification possible
       
         $HigherTaxon = $HigherTaxon1->get_elements_by_tagname('HigherTaxonName');
         $TaxonRank = $HigherTaxon1->get_elements_by_tagname('HigherTaxonRank');
       
        if($HigherTaxon) {
   //      echo "Higher Taxon: " .$HigherTaxon[0]->get_content()." (".$TaxonRank[0]->get_content().")<br>";
         $sqlHigherTaxon[] = $HigherTaxon[0]->get_content(); }
 
        if($TaxonRank) {
         $sqlHigherTaxonRank[]  = $TaxonRank[0]->get_content(); }

      } //foreach $HugherTaxa
    
     foreach ($ScientificNames as $ScientificName) {
    
   //  $ScientificNamesAtomized = $ScientificName->get_elements_by_tagname('NameAtomised');

//     foreach ($ScientificNamesAtomized as $ScientificNameAtomized) {
    
      $Bacteria = $ScientificName->get_elements_by_tagname('Bacterial');
      $Botany = $ScientificName->get_elements_by_tagname('Botanical');
      $Zoology = $ScientificName->get_elements_by_tagname('Zoological');   
      $Virology = $ScientificName->get_elements_by_tagname('Viral');         
      

      if($Bacteria) {

        foreach ($Bacteria as $Bacterical) {
      
         $GenusBac = $Bacterical->get_elements_by_tagname('GenusOrMonomial');
         $SubgenusBac = $Bacterical->get_elements_by_tagname('Subgenus');
         $SpeciesEpithetBac = $Bacterical->get_elements_by_tagname('SpeciesEpithet');
         $SubspeciesEpithetBac = $Bacterical->get_elements_by_tagname('SubspeciesEpithet');
        
          if($GenusBac) {
  //       echo "Genus: " . $GenusBac[0]->get_content() . "<br>";
         $sqlGenus[] = $GenusBac[0]->get_content(); }
          if($SubgenusBac) {
  //       echo "Subgenus: " . $SubgenusBac[0]->get_content() . "<br>";
         $sqlSubgenus[] = $SubgenusBac[0]->get_content(); }
          if($SpeciesEpithetBac) {
   //      echo "Spec.Epi: " . $SpeciesEpithetBac[0]->get_content() . "<br>";
         $sqlFirstEpithet[] = $SpeciesEpithetBac[0]->get_content(); }
          if($SubspeciesEpithetBac) {
   //      echo "SspEpi: " . $SubspeciesEpithetBac[0]->get_content() . "<br>";
         $sqlSecondEpithet[] = $SubspeciesEpithetBac[0]->get_content(); }
         
         if(empty($sqlGenus) and empty($sqlSubgenus) and empty($sqlFirstEpithet) and empty($sqlSubspecies))
         {              
   //      echo "Bacteria_All: " . $Bacteria[0]->get_content() . "<br>"; //if (empty -> $GenusBac, $SubgenusBac, $SpeciesEpithetBac, $SubspeciesEpithetBac)      
         $sqlName_All[] = $Bacteria[0]->get_content();    }     

        } //foreach $Bacteria
      } //if($Bacteria)

      if($Botany) {
      
        foreach ($Botany as $Botanical) {
        
          $GenusBot = $Botanical->get_elements_by_tagname('GenusOrMonomial');
          $FirstEpithet = $Botanical->get_elements_by_tagname('FirstEpithet');
          $SecondEpithet = $Botanical->get_elements_by_tagname('InfraspecificEpithet');
          $Rank = $Botanical->get_elements_by_tagname('Rank');
          $HybridFlag = $Botanical->get_elements_by_tagname('HybridFlag');
        
          if($GenusBot) {
   //       echo "Genus: " . $GenusBot[0]->get_content() . "<br>";
          $sqlGenus[] = $GenusBot[0]->get_content(); }
          if($SubgenusBot) {
   //       echo "Spec.Epi: " . $FirstEpithet[0]->get_content() . "<br>";
          $sqlFirstEpithet[] = $FirstEpithet[0]->get_content(); }
          if($Rank) {
  //        echo "Rank: " . $Rank[0]->get_content() . "<br>";            
          $sqlRank[] = $Rank[0]->get_content(); }
          if($SecondEpithet) {        
   //       echo "Sec.Epi: " . $SecondEpithet[0]->get_content() . "<br>";    
          $sqlSecondEpithet[] = $SecondEpithet[0]->get_content(); }
          if($HybridFlag) {
   //       echo "Hybrid: " . $HybridFlag[0]->get_content() . "<br>";
          $sqlHybridFlag[] = $HybridFlag[0]->get_content(); }
          
          if(empty($sqlGenus) and empty($sqlFirstEpithet) and empty($sqlRank) and empty($sqlSecondEpithet))
          {        
  //        echo "Botany_All: " . $Botany[0]->get_content() . "<br>"; //if (empty -> $GenusBot, $FirstEpithet, $SecondEpithet, $Rank, $HybridFlag)      
          $sqlName_All[] = $Botany[0]->get_content();   }
      
        } //foreach $Botany
      } //if($Botany)
      
      if($Zoology) {
      
        foreach ($Zoology as $Zoological => $Zoo) {
      
          $GenusZoo = $Zoo->get_elements_by_tagname('GenusOrMonomial');
          $SubgenusZoo = $Zoo->get_elements_by_tagname('Subgenus');
          $SpeciesEpithetZoo = $Zoo->get_elements_by_tagname('SpeciesEpithet');
          $SubspeciesEpithetZoo = $Zoo->get_elements_by_tagname('SubspeciesEpithet');

          if($GenusZoo) {
   //       echo "Genus: " .$GenusZoo[0]->get_content()."<br>"; 
          $sqlGenus[] = $GenusZoo[0]->get_content(); }
          if($SubgenusZoo) {
   //       echo "Subgenus: " . $SubgenusZoo[0]->get_content() . "<br>";
          $sqlSubgenus[] = $SubgenusZoo[0]->get_content(); }
          if($SpeciesEpithetZoo) {
  //        echo "Spec.Epi: " . $SpeciesEpithetZoo[0]->get_content() . "<br>"; 
          $sqlFirstEpithet[] = $SpeciesEpithetZoo[0]->get_content(); }
          if($SubspeciesEpithetZoo) {
   //       echo "SspEpi: " . $SubspeciesEpithetZoo[0]->get_content() . "<br>";
          $sqlSecondEpithet[] = $SubspeciesEpithetZoo[0]->get_content(); }
          
          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[0]->get_content(); }
      
        } //foreach $Zoology
      } //if($Zoology)
      
      if($Virology)
      {
      
        foreach ($Virology as $Viral) {
        
          $GenusV = $Viral->get_elements_by_tagname('GenusOrMonomial');
        
          if($GenusV) {
   //       echo "Genus: " . $GenusV[0]->get_content() . "<br>";
          $sqlGenus[] = $GenusV[0]->get_content(); }
          if(empty($sqlGenus)) 
          {              
   //       echo "Virology_All: " . $Virology[0]->get_content() . "<br>";
          $sqlName_All[] = $Virology[0]->get_content(); }
      
        } //foreach $Virology
      } //if($Virology)
    
  //  } //foreach $ScientificNamesAtomized
    
    } //foreach $ScientificNames
    
  } //foreach $TaxaIdentified
  
  } //foreach $Identifications
  
/*----------------------------------------MULTI MEDIA OBJECTS -----------------------------*/
  $MultiMediaObjects = $Unit->get_elements_by_tagname('MultiMediaObject');

foreach ($MultiMediaObjects as $IndexMultiMediaObjects => $MultiMediaObject) {     // more than one Identification possible
  
     $FileURI = $MultiMediaObject->get_elements_by_tagname('FileURI');
     $ProductURI = $MultiMediaObject->get_elements_by_tagname('ProductURI');
     
     if($FileURI) {
     $sqlFileURI[] = $FileURI[0]->get_content(); }
     if($ProductURI) {
     $sqlProductURI[] = $ProductURI[0]->get_content(); }
     
  }   // 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
 
?>