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cls_oai.php
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<?php
class oai{
var $allowedprefixes=array('oai_dc','pan_dc');
#$possiblearguments=array('verb','metadataPrefix','resumptionToken');
var $gatewayfolder='ABCD';
var $repositoryname=null;
var $providerinfo=array(); //harvested provider info as delivered by biocase monitoring service
var $repositories=array();//sets
var $modifieddates=array();
var $error=false;
var $setspec=false;//is a set specified?
function __construct($from=null, $until=null){
$this->getRepositories($from, $until);
#print_r($this->repositories['name']);exit;
# $this->GetModifiedDates();
}
function getServerURL() {
$url = (isset($_SERVER[HTTPS]) && $_SERVER[HTTPS]=='on') ? 'https://' : 'http://';
return $url.$_SERVER[HTTP_HOST];
}
function getRequestHeaderXML() {
$requesturl = $this->getServerURL().parse_url('http://localhost'.$_SERVER[REQUEST_URI], PHP_URL_PATH);
$xml = '<?xml version="1.0" encoding="UTF-8"?><OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd">';
$xml .= '<responseDate>'.gmdate('Y-m-d\TH:i:s\Z').'</responseDate>';
$xml .= '<request';
foreach ($_GET as $key => $value) {
$xml .= ' '.htmlspecialchars($key).'="'.htmlspecialchars($value).'"';
}
$xml .= '>'.htmlspecialchars($requesturl).'</request>';
return $xml;
}
function getError($errcode,$errmessage=''){
echo $this->getRequestHeaderXML().'<error code="'.$errcode.'">'.htmlspecialchars($errmessage).'</error></OAI-PMH>';
$this->error=true;
}
function getProviderInfo(){
$providers=json_decode(file_get_contents($this->gatewayfolder.'/archives.txt'));
foreach($providers as $provider){
#echo basename($provider->link);
#echo substr(basename($provider->xml_archive),0,-4).'=='.$this->repositoryname."\r\n";exit;
if($provider->archive_folder==$this->repositoryname){
$this->providerinfo=$provider;
}
}
}
function getRepositories($from=null, $to=null){
$earliesttimestamp=10000000000000000;
unset($this->repositories);
$providerinfo=json_decode(file_get_contents($this->gatewayfolder.'/archives.txt'));
# $providerinfo=array_merge($providerinfo,json_decode(file_get_contents($this->gatewayfolder.'/deleted.txt')));
#print_r($providerinfo);exit;
foreach($providerinfo as $pk=>$provider){
# echo strtotime($from).' < '.strtotime($provider->harvest_time).'> '.strtotime($to).'<br>'."\r\n";
$harvest=true;
if(isset($from)){
if(strtotime($provider->harvest_time)>=strtotime($from)){
$harvest=true;
}else $harvest=false;
}
if(isset($to)){
if(strtotime($provider->harvest_time)<=strtotime($to)){
$harvest=true;
}else $harvest=false;
}
if($provider->harvest_status=='delete'){ $harvest=true;}
if($harvest===true){
if(strtotime($provider->harvest_time)<$earliesttimestamp)
$this->earliesttimestamp=$provider->harvest_time;
if(trim($provider->archive_folder)!='')
$this->repositories[$pk]=$provider->archive_folder;
}
} #print_r($this->repositories); exit;
sort($this->repositories);
}
function GetArchivesFiles(){
$archivefiles=array();
if(sizeof($this->repositories)>0){
foreach($this->repositories as $rid=>$rep){
#echo $this->gatewayfolder.'/'.$rep;
$files = scandir($this->gatewayfolder.'/'.$rep);
foreach($files as $file){
if(strpos($file,'.xml')){
$archivefiles[]=$this->gatewayfolder.'/'.$rep.'/'.$file;
}
}
}}
return $archivefiles;
}
static function getDatasetId($file){
return $file;
}
function GetModifiedDates(){
$date=date('Y-m-d');
$dirinfo=$this->fopendir($this->gatewayfolder.'/'.$this->repositoryname);
foreach($dirinfo as $file){
if(file_exists($file)){
$this->modifieddates[basename($file)]=date('Y-m-d',filemtime($file));
#$xml=
#$xml=file_get_contents($file,false,null,0, 2048);
#if(preg_match('!<abcd:DateModified>(.*?)</abcd:DateModified>!s',$xml,$match)){
# $this->modifieddates[basename($file)]=$this->convertdate($match[1]);
#}
#else $this->modifieddates[basename($file)]=$date;
}
}
}
function ListSets(){
$response=$this->getRequestHeaderXML().'<ListSets>';
foreach($this->repositories as $sid=>$set){
if($set['status']!='delete'){
$response.='<set>
<setSpec>'.trim($set).'</setSpec>
<setName>'.trim($set).'</setName>
</set>';
}
}
$response.='</ListSets>
</OAI-PMH>';
return $response;
}
function Identify(){
$response=$this->getRequestHeaderXML().'<Identify>
<repositoryName>GFBio ABCD Archives OAI Provider</repositoryName>
<baseURL>'.$requesturl.'</baseURL>
<protocolVersion>2.0</protocolVersion>
<adminEmail>[email protected]</adminEmail>
<earliestDatestamp>'.$this->earliesttimestamp.'</earliestDatestamp>
<deletedRecord>transient</deletedRecord>
<granularity>YYYY-MM-DDThh:mm:ssZ</granularity>';
$response.='</Identify>
</OAI-PMH>';
return $response;
}
function ListMetadataFormats(){
$response=$this->getRequestHeaderXML().'<ListMetadataFormats>
<metadataFormat>
<metadataPrefix>oai_dc</metadataPrefix>
<schema>http://www.openarchives.org/OAI/2.0/oai_dc.xsd</schema>
<metadataNamespace>http://www.openarchives.org/OAI/2.0/oai_dc/</metadataNamespace>
</metadataFormat>
<metadataFormat>
<metadataPrefix>pan_dc</metadataPrefix>
<schema>http://ws.pangaea.de/schemas/pansimple/pansimple.xsd</schema>
<metadataNamespace>http://ws.pangaea.de/schemas/pansimple/</metadataNamespace>
</metadataFormat>
</ListMetadataFormats>
</OAI-PMH>';
return $response;
}
function checkResumtionToken($resumptiontoken=null,$from=null, $until=null){
if(!file_exists($this->gatewayfolder.'/tokens'))
mkdir($this->gatewayfolder.'/tokens');
$alltokens=scandir($this->gatewayfolder.'/tokens');
foreach($alltokens as $oldtoken){
if ($oldtoken!='.'&&$oldtoken!='..')
if((time()-filemtime($this->gatewayfolder.'/tokens/'.$oldtoken))>30000)
unlink($this->gatewayfolder.'/tokens/'.$oldtoken);
}
if($resumptiontoken!=null){
if(file_exists($this->gatewayfolder.'/tokens/'.$resumptiontoken)){
$tokeninfostr=file_get_contents($this->gatewayfolder.'/tokens/'.$resumptiontoken);
#unlink($this->gatewayfolder.'/tokens/'.$resumptiontoken);
$tokeninfo=json_decode($tokeninfostr,true);
if(isset($tokeninfo['repositoryname'])){
$ret['repositoryname']=$this->repositoryname=$tokeninfo['repositoryname'];
}
if(isset($tokeninfo['from']) || isset($tokeninfo['until'])){
$ret['from']=$tokeninfo['from'];
$ret['until']=$tokeninfo['until'];
$this->getRepositories($tokeninfo['from'], $tokeninfo['until']);
if(!isset($this->repositoryname))
$this->repositoryname=$this->repositories[0];
}
}else{
$this->getError('badResumptionToken','Could not find Token');exit;
}
}else{
if(isset($from))
$ret['from']=$from;
if(isset($until))
$ret['until']=$until;
$this->getRepositories($from, $until);
if(!isset($this->repositoryname))
$this->repositoryname=$this->repositories[0];
}
$nexttoken=uniqid();
$fileinfo=$this->GetArchivesFiles();
#print_r($fileinfo);exit;
sort($fileinfo);
if(!isset($resumptiontoken)){
$ret['firstfile']=1;
//with set spec
if(isset($this->repositoryname)){
if(file_exists($this->gatewayfolder.'/'.$this->repositoryname.'/response.00001.xml')){
$currentfile=$this->gatewayfolder.'/'.$this->repositoryname.'/response.00001.xml';
}
if(file_exists($this->gatewayfolder.'/'.$this->repositoryname.'/response.00002.xml')){
$nextfile=$this->gatewayfolder.'/'.$this->repositoryname.'/response.00002.xml';
#$nexttoken=md5($this->gatewayfolder.'/'.$this->repositoryname.'/response.00002.xml').$postfix;
}else $nextfile=$fileinfo[1];
}elseif(sizeof($fileinfo)==0){
$nexttoken=null;
$currentfile=null;
}
else{
$currentfile=$fileinfo[0];
$nextfile=$fileinfo[1];
#$nexttoken=md5($fileinfo[1]).$postfix;
}
}else{
$ret['firstfile']=0;
foreach($fileinfo as $kf=>$fi){
if(preg_match('/^'.$this->gatewayfolder.'\/(.*?)\//s',$fileinfo[$kf+1],$fma)){
$currentarchive=trim($fma[1]);
}
if($fi==$tokeninfo['nextfile']){
$currentfile=$fi;
if(strpos($currentfile,'00001.xml')!==false)
$ret['firstfile']=1;
#if(isset($fileinfo[$kf+1])){
# if (str_replace(substr(strrchr($fileinfo[$kf+1], '/'), 1),'',$fileinfo[$kf+1])
# ==str_replace(substr(strrchr($fileinfo[$kf], '/'), 1),'',$fileinfo[$kf])){
#$nexttoken=md5($fileinfo[$kf+1]).$postfix;
$nextfile=$fileinfo[$kf+1];
# }
# }
}
}
}
if(isset($currentfile)){
$this->repositoryname= basename(dirname($currentfile));
$this->getProviderInfo();
$ret['file']=$currentfile;
if(isset($nextfile)){
$ret['nextfile']=$nextfile;
$ret['nexttoken']=$nexttoken;
file_put_contents($this->gatewayfolder.'/tokens/'.$nexttoken, json_encode($ret));
}
#print_r($ret);exit;
return $ret;
}
else return false;
}
function ListIdentifiers($resumptiontoken=null,$from=null, $to=null){
$xsltfile='abcd2ids.xslt';
$n=0;
if(isset($from)){
$fromts=strtotime($from);
if($fromts===false)
{echo $this->getError('badArgument','Invalid date format');exit;}
}
if(isset($to)){
$tots=strtotime($to);
if($fromts===false)
{echo $this->getError('badArgument','Invalid date format');exit;}
}
if(isset($tots)&&isset($fromts)){
if($tots<$fromts)
{echo $this->getError('badArgument','From date until date');exit;}
else{
}
}
$tokeninfo=$this->checkResumtionToken($resumptiontoken, $from, $to);
if(!$tokeninfo)echo $this->getError('badResumptionToken');
else{
$xmlfile=$tokeninfo['file'];
$resumptiontoken=$tokeninfo['nexttoken'];
if(isset($xmlfile)){
$response= $this->getRequestHeaderXML().'<ListIdentifiers>';
if($xmlfile!='..'&&$xmlfile!='.'&&strpos($xmlfile,'.xml')!==false){libxml_use_internal_errors(true);
$XML = new DOMDocument();
$xmlstr=file_get_contents('./'.$xmlfile);
//brutal..
if($xmlstr===false) { echo $this->getError('Internal Error','Problems accessing file : '.$xmlfile);exit; }
#print($xmlfile);
if(strpos($xmlstr,'xmlns:abcd21')!==false){
$xmlstr=str_replace('abcd21="http://www.tdwg.org/schemas/abcd/2.1','abcd="http://www.tdwg.org/schemas/abcd/2.06',$xmlstr);
$xmlstr=str_replace('abcd21','abcd',$xmlstr);
}
$XML->loadXML($xmlstr);
$xslt = new XSLTProcessor();
$xslt->registerPhpFunctions();
$XSL = new DOMDocument();
$XSL->load( $xsltfile, LIBXML_NOCDATA);
$xslt->importStylesheet( $XSL );
$xsltres=$xslt->transformToXML( $XML );
if($xsltres!==false&&$xsltres!=null){
$response.= str_replace('<?xml version="1.0" encoding="UTF-8"?>','',$xsltres);
}
else {
$libxmlerror='';
foreach (libxml_get_errors() as $error) {
echo $libxmlerror.= "Libxml error: {$error->message}\n";
}
echo $this->getError('Internal Error','XSLT Processing : '.$libxmlerror);exit;
}
libxml_use_internal_errors(false);
$n++;
}else {
echo $this->getError('Internal Error','file does not exist: '.$xsltfile);exit;
}
if(isset($resumptiontoken))
$response.= '<resumptionToken>'.$resumptiontoken.'</resumptionToken>';
else $response.= '<resumptionToken/>';
echo $response.='</ListIdentifiers>
</OAI-PMH>';
#echo $response;
}else echo $this->getError('Internal Error','XML Missing: '.$xmlfile);exit;
}
}
function ListRecords($resumptiontoken=null,$from=null, $to=null,$format='oai_dc'){
$xmloutput='';
if($format=='oai_dc')
$xsltfile='abcd2pansimple.xslt';
elseif($format=='pan_dc')
$xsltfile='abcd2pansimple.xslt';
$xsltfile2='abcdmetadata2pansimple.xslt';
$xsltfiledel='abcd_deleted.xslt';
if(isset($from)){
$fromts=strtotime($from);
if($fromts===false)
{echo $this->getError('badArgument','Invalid date format');exit;}
}
if(isset($to)){
$tots=strtotime($to);
if($fromts===false)
{echo $this->getError('badArgument','Invalid date format');exit;}
}
if(isset($tots)&&isset($fromts)){
if($tots<$fromts)
{echo $this->getError('badArgument','From date until date');exit;}
else{
}
}
if($resumptiontoken==null) $firstfile=true;
else $firstfile=false;
$tokeninfo=$this->checkResumtionToken($resumptiontoken, $from, $to);
$firstfile=$tokeninfo['firstfile'];
if($tokeninfo['file']==null)$this->getError('noRecordsMatch');
elseif(!$tokeninfo)echo $this->getError('badResumptionToken');
else{
$xmlfile=$tokeninfo['file'];
$resumptiontoken=$tokeninfo['nexttoken'];
if(isset($xmlfile)){
$xmloutput= $this->getRequestHeaderXML().'<ListRecords>';
if($xmlfile!='..'&&$xmlfile!='.'&&strpos($xmlfile,'.xml')!==false){
$XML = new DOMDocument();
$xmlstr=file_get_contents($xmlfile);
if($xmlstr===false) {echo $this->getError('Internal Error','Problems accessing file : '.$xmlfile);exit; }
//brutal..
if(strpos($xmlstr,'xmlns:abcd21')!==false){
$xmlstr=str_replace('abcd21="http://www.tdwg.org/schemas/abcd/2.1','abcd="http://www.tdwg.org/schemas/abcd/2.06',$xmlstr);
$xmlstr=str_replace('abcd21','abcd',$xmlstr);
}
$xmlparts=explode('Metadata>',$xmlstr);
$xmlheader=$xmlparts[0].'Metadata>';
$xmlbody=$xmlparts[1].'Metadata>'.$xmlparts[2];
//enriching ABCD content with info from e.g biocase monitor service
#print_r($this->providerinfo);exit;
$xmlheader=preg_replace('/<([a-z]+:)?DataSets\s{1}/','$0xmlns:so="https://ws.gfbio.org/so/" ',$xmlheader);
$xmlheader=preg_replace('/DataSet>/','DataSet>
<so:ABCDFile>'.htmlspecialchars($this->getServerURL().'/'.basename($_SERVER[SCRIPT_NAME]).'/'.dirname($xmlfile)).'</so:ABCDFile>
<so:ABCDFiletime>'.date('Y-m-d\TH:i:s\Z',filemtime(dirname($xmlfile))).'</so:ABCDFiletime>
<so:ABCDHarvesttime>'.date('Y-m-d\TH:i:s\Z',strtotime($this->providerinfo->harvest_time)).'</so:ABCDHarvesttime>
<so:BMS_ArchiveUrl>'.$this->providerinfo->archive_url.'</so:BMS_ArchiveUrl>
<so:BMS_ArchiveFolder>'.$this->providerinfo->archive_folder.'</so:BMS_ArchiveFolder>
<so:BMS_Datacenter>'.$this->providerinfo->provider_datacenter.'</so:BMS_Datacenter>
<so:BMS_Datacenter_short>'.$this->providerinfo->provider_shortname.'</so:BMS_Datacenter_short>
<so:BMS_Publisher>'.$this->providerinfo->provider_name.'</so:BMS_Publisher>
<so:BMS_dsa>'.$this->providerinfo->dsa.'</so:BMS_dsa>
<so:BMS_ProviderID>'.$this->providerinfo->providerid.'</so:BMS_ProviderID>
<so:BMS_Pywrapper>'.$this->providerinfo->biocase_url.'</so:BMS_Pywrapper>
<so:BMS_Querytool>'.$this->providerinfo->querytool.'</so:BMS_Querytool>',$xmlheader);
echo $xmloutput;
$xmlstr=$xmlheader.$xmlbody;
$XML->loadXML($xmlstr);
if($this->providerinfo->harvest_status=="delete"){
$xslt = new XSLTProcessor();
$xslt->registerPhpFunctions();
$XSL = new DOMDocument();
$XSL->load( $xsltfiledel, LIBXML_NOCDATA);
$xslt->importStylesheet( $XSL );
echo str_replace('<?xml version="1.0" encoding="UTF-8"?>','',$xslt->transformToXML( $XML ));
}
else{
if($firstfile==1){
$xslt2 = new XSLTProcessor();
$xslt2->registerPhpFunctions();
$XSL2 = new DOMDocument();
$XSL2->load( $xsltfile2, LIBXML_NOCDATA);
$xslt2->importStylesheet( $XSL2 );
echo str_replace('<?xml version="1.0" encoding="UTF-8"?>','',$xslt2->transformToXML( $XML ));
}
$xslt = new XSLTProcessor();
$xslt->registerPhpFunctions();
$XSL = new DOMDocument();
$XSL->load( $xsltfile, LIBXML_NOCDATA);
$xslt->importStylesheet( $XSL );
$xsltresult=$xslt->transformToXML( $XML );
echo str_replace('<?xml version="1.0" encoding="UTF-8"?>','',$xsltresult);
}
}
if(isset($resumptiontoken)) {
echo '<resumptionToken>'.$resumptiontoken.'</resumptionToken>';
}
echo '</ListRecords></OAI-PMH>';
}
}
}
static function convertdate($datestr){
$timestamp=strtotime($datestr);
if($timestamp!==false){
return date('Y-m-d\TH:i:s\Z',$timestamp);
}
else return '';
}
static function CamelcaseToWords($string){
return strtolower(implode(' ', preg_split('/(?=[A-Z])/',$string)));
}
static function GetLandingPage($providerid,$dsa,$cat){
//calling biocase monitor
//http://bms.gfbio.org/services/landingpages/?output=json&provider=2&dsa=BSMeryscoll&filter=&inst=&col=&cat=M-0014086+%2F+14380+%2F+9132
$bmsinfo=json_decode(file_get_contents('http://bms.gfbio.org/services/landingpages/?output=json&provider='.$providerid.'&dsa='.$dsa.'&cat='.$cat));
return 'http://bms.gfbio.org/services/landingpages/?output=json&provider='.$providerid.'&dsa='.$dsa.'&cat='.$cat.' '.$bmsinfo->dataUnit;
}
function fopendir($dir, &$fileinfo = array()) {
if ($handle = opendir($dir)) {
while (false !== ($file = readdir($handle))) {
if (!is_dir($dir.'/'.$file)) {
$fileinfo[] = $dir.'/'.$file;
} elseif (is_dir($dir.'/'.$file) && $file != '.' && $file != '..') {
$this->fopendir($dir.'/'.$file, $fileinfo);
}
}
closedir($handle);
}
return $fileinfo;
}
}//class
?>