<!-- 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);

$Datasets = $dom->get_elements_by_tagname('DataSet');

foreach ($Datasets as $Dataset) {

  $SourceInstitutionCode = $Dataset->get_elements_by_tagname('SourceInstitutionCode');
  $SourceName = $Dataset->get_elements_by_tagname('SourceName');

//  echo "Source Institution: " . $sqlSourceInstitutionCode . "<br>";
//  echo "Source Collection: " . $SourceName[0]->get_content() . "<br>"; 
  $sqlSourceInstitutionCode = addslashes(utf8_decode($SourceInstitutionCode[0]->get_content()));
  $sqlSourceName = addslashes(utf8_decode($SourceName[0]->get_content())); 

$Units = $Dataset->get_elements_by_tagname('Unit');

foreach ($Units as $Unit) {

  $UnitID = $Unit->get_elements_by_tagname('UnitID');
  $GatheringNo = $Dataset->get_elements_by_tagname('CollectorsFieldNumber');
  
 // echo "Unit ID: " . $UnitID[0]->get_content() . "<br>";
  $sqlUnitID = $UnitID[0]->get_content();
  $sqlGatheringNo = $GatheringNo[0]->get_content();  

/*----------------------------GATHERING---------------------------------------------------------*/
  
  $Gatherings = $Unit->get_elements_by_tagname('Gathering');

  foreach ($Gatherings as $Gathering) {

    $GatheringDate = $Gathering->get_elements_by_tagname('DateText');
    $GatheringDateAll = $Gathering->get_elements_by_tagname('GatheringDateTime');  //if (empty($GatheringDate))
    $GatheringISODateTimeBegin = $Gathering->get_elements_by_tagname('ISODateTimeBegin');
    $GatheringDayNumberBegin = $Gathering->get_elements_by_tagname('DayNumberBegin');
    $GatheringTimeOfDayBegin = $Gathering->get_elements_by_tagname('ISOTimeOfDayBegin');    
    $GatheringISODateTimeEnd = $Gathering->get_elements_by_tagname('ISODateTimeEnd');
    $GatheringDayNumberEnd = $Gathering->get_elements_by_tagname('DayNumberEnd');
    $GatheringTimeOfDayEnd = $Gathering->get_elements_by_tagname('TimeOfDayEnd');
    $GatheringAgents = $Gathering->get_elements_by_tagname('GatheringAgent');
    $GatheringSites = $Gathering->get_elements_by_tagname('GatheringSite');
  
    if(empty($GatheringDate)) {
      if($GatheringDateAll) {
  //  echo "Date2: " . $GatheringDateAll[0]->get_content() . "<br>";  //if (empty($GatheringDate))
    $sqlGatheringDate = addslashes($GatheringDateAll[0]->get_content()); }}
    else {
  //  echo "Date: " . $GatheringDate[0]->get_content() . "<br>";
      if($GatheringDate) {
    $sqlGatheringDate = addslashes($GatheringDate[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('PersonName');
      $AgentText = $GatheringAgent->get_elements_by_tagname('AgentText');   //if (empty($GatheringAgent)
      
      if(empty($GatheringAgent)) {
        if($AgentText) {
   //     echo "Person2: " . $AgentText[0]->get_content() . "<br>";
        $sqlPersonName = addslashes($AgentText[0]->get_content()); }}

      else {
        if($PersonName) {
  //      echo "Person: " . $PersonName[0]->get_content() . "<br>"; 
        $sqlPersonName = addslashes($PersonName[0]->get_content()); }} }
  
    foreach ($GatheringSites as $GatheringSite) {
  
      $LocalityText = $GatheringSite->get_elements_by_tagname('LocalityText');
      $ContinentOrOcean = $GatheringSite->get_elements_by_tagname('ContinentOrOcean');
      $CountryName = $GatheringSite->get_elements_by_tagname('CountryName');
      $Country = $GatheringSite->get_elements_by_tagname('Country');  //if (empty($CountryName))
      $ISO2 = $GatheringSite->get_elements_by_tagname('ISO2Letter');
      $NamedArea = $GatheringSite->get_elements_by_tagname('NamedArea');  //if (empty($Country))
      $NearNamedPlaces = $GatheringSite->get_elements_by_tagname('NearNamedPlaces');  //if (empty($Country))
      $LongitudeDecimal = $GatheringSite->get_elements_by_tagname('LongitudeDecimal');
      $LatitudeDecimal = $GatheringSite->get_elements_by_tagname('LatitudeDecimal');
      $SiteCoordinates = $GatheringSite->get_elements_by_tagname('SiteCoordinates');  //if (empty($LongitudeDecimal & LatitudeDecimal))  
      $Altitude = $GatheringSite->get_elements_by_tagname('Altitude');
  
      if($LocalityText) {
  //    echo "Locality: " . $LocalityText[0]->get_content() . "<br>"; 
      $sqlLocalityText = addslashes($LocalityText[0]->get_content()); }
      if($ContinentOrOcean) {
  //    echo "Continent: " . $ContinentOrOcean[0]->get_content() . "<br>"; 
      $sqlContinentOrOcean = addslashes($ContinentOrOcean[0]->get_content()); }
      

      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($NamedArea)) {
        if($NearNamesPlaces) {
  //      echo "NearNamedPlaces: " . $NearNamedPlaces[0]->get_content() . "<br>";
        $sqlGatheringOther = addslashes($NearNamedPlaces[0]->get_content()); }
        }
        
        else {
       if(!empty($GatheringOther)) {
 //       echo "NamedAreas: " . $NamedAreas[0]->get_content() . "<br>";
        $sqlGatheringOther = addslashes($NamedAreas[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(); }
 //     echo "Coordinates: " . $SiteCoordinates[0]->get_content() . "<br>";
      if($Altitude) {
  //    echo "Altitude: " . $Altitude[0]->get_content() . "<br>";
      $sqlAltitude = addslashes($Altitude[0]->get_content()); }
    } // foreach $GatheringSites
  } //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');
  
   // foreach ($TaxaIdentified as $TaxonIdentified) {
  
     $NameAuthorYearString = $Identification->get_elements_by_tagname('NameAuthorYearString');            // Name, Author, Year
     $ScientificNamesAtomized = $Identification->get_elements_by_tagname('ScientificNameAtomized');
     $HigherTaxa = $Identification->get_elements_by_tagname('HigherTaxon');     

      if($NameAuthorYearString) {
//     echo "Name All: " . $NameAuthorYearString[0]->get_content() . "<br>";
     $sqlNameAuthorYearString[] = addslashes($NameAuthorYearString[0]->get_content()); }
     if($Identification) {
 //    echo "Preferred: " . $Identification->get_attribute('PreferredIdentificationFlag') . "<br>";
     $sqlPreferredIdentificationFlag[] = $Identification->get_attribute('PreferredIdentificationFlag'); }

      foreach ($HigherTaxa as $index => $HigherTaxon) { // more than one HigherTaxon per Identification possible
       
       if($HigherTaxon) {
 //        echo "Higher Taxon: " .$HigherTaxon." (".$HigherTaxon->get_attribute('TaxonRank').")<br>";
         $sqlHigherTaxon[] = $HigherTaxon; 
         $sqlHigherTaxonRank[]  = $HigherTaxon->get_attribute('TaxonRank'); }

      } //foreach $HugherTaxa
    
     foreach ($ScientificNamesAtomized as $ScientificNameAtomized) {
    
      $Bacteria = $ScientificNameAtomized->get_elements_by_tagname('Bacterial');
      $Botany = $ScientificNameAtomized->get_elements_by_tagname('Botanical');
      $Zoology = $ScientificNameAtomized->get_elements_by_tagname('Zoological');   
      $Virology = $ScientificNameAtomized->get_elements_by_tagname('Viral');         
      

      if($Bacteria) {

        foreach ($Bacteria as $Bacterical) {
      
         $GenusBac = $Bacterical->get_elements_by_tagname('Genus');
         $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('Genus');
          $FirstEpithet = $Botanical->get_elements_by_tagname('FirstEpithet');
          $SecondEpithet = $Botanical->get_elements_by_tagname('SecondEpithet');
          $Rank = $Botanical->get_elements_by_tagname('Rank');
          $HybridFlag = $Botanical->get_elements_by_tagname('HybridFlag');
        
          if($GenusBot) {
  //        echo "Genus: " . $GenusBot[0]->get_content() . "<br>";
          $sqlGenus[] = $GenusBot[0]->get_content(); }
          if($FirstEpithet) {
 //         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('Genus');
          $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 . "<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('Genus');
        
          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 $TaxaIdentified
  
  } //foreach $Identifications
  
/*----------------------------------------MULTI MEDIA OBJECTS -----------------------------*/
  $MultiMediaObjects = $Unit->get_elements_by_tagname('UnitDigitalImage');

foreach ($MultiMediaObjects as $IndexMultiMediaObjects => $MultiMediaObject) {     // more than one Identification possible
  
     $FileURI = $MultiMediaObject->get_elements_by_tagname('ImageURI');
     
     if($FileURI) {
     $sqlFileURI[] = $FileURI[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


} //foreach $Datasets

?>