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ops_ims.class.php
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ops_ims.class.php
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<?php
require_once 'exceptions.inc.php';
define('REQUEST_URI_NO', 40);
class OpsIms {
private $_request;
var $IMS_variables = array(
'?chembl_target_uri'=>'http://rdf.ebi.ac.uk/resource/chembl/target/' ,
'?chembl_compound_uri'=>'http://rdf.ebi.ac.uk/resource/chembl/molecule/' ,
'?uniprot_target_uri'=>'http://purl.uniprot.org/uniprot/' ,
'?cw_target_uri'=>'http://www.conceptwiki.org/concept/' ,
'?cw_compound_uri'=>'http://www.conceptwiki.org/concept/' ,
'?ocrs_compound_uri'=>'http://chemistry.openphacts.org/OPS' ,
'?db_compound_uri'=>'http://bio2rdf.org/drugbank',
'?db_target_uri'=>'http://bio2rdf.org/drugbank',
'?dg_gene_uri' => 'http://identifiers.org/ncbigene/',
'?umls_disease_uri' => 'http://linkedlifedata.com/resource/umls/id/',
'?node_uri' => 'http://rdf.ebi.ac.uk/resource/chembl/protclass/&targetUriPattern=http://purl.obolibrary.org/obo/CHEBI_&targetUriPattern=http://purl.uniprot.org/enzyme/&targetUriPattern=http://purl.obolibrary.org/obo/GO_&targetUriPattern=http://www.bioassayontology.org/bao#BAO_&targetUriPattern=http://purl.obolibrary.org/obo/DOID_',
'?aers_compound_uri' => 'http://aers.data2semantics.org/resource/drug/',
'?patent_uri' => 'http://rdf.ebi.ac.uk/resource/surechembl/patent/',
'?pw_uri' => 'http://identifiers.org/wikipathways/',
'?pw_compound_uri' => '',
'?pw_target_uri' => '',
'?pw_entity_uri' => '',
'?pw_ref_uri' => 'http://identifiers.org/pubmed/',
'?schembl_target_uri' => 'http://rdf.ebi.ac.uk/resource/surechembl/target/',
'?schembl_compound_uri' => 'http://rdf.ebi.ac.uk/resource/surechembl/molecule/',
'?schembl_disease_uri' => 'http://rdf.ebi.ac.uk/resource/surechembl/indication/',
'?oidd_assay_uri' => 'http://openinnovation.lilly.com/bioassay#',
'?chembl_assay_uri' => 'http://rdf.ebi.ac.uk/resource/chembl/assay/',
'?nextprot_target_uri' => 'http://www.nextprot.org/db/search#'
);
var $IMS_interm_variables = array(
'?ims_chembl_target_uri'=>'http://rdf.ebi.ac.uk/resource/chembl/target/' ,
'?ims_chembl_compound_uri'=>'http://rdf.ebi.ac.uk/resource/chembl/molecule/' ,
'?ims_uniprot_target_uri'=>'http://purl.uniprot.org/uniprot/' ,
'?ims_cw_target_uri'=>'http://www.conceptwiki.org/concept/' ,
'?ims_cw_compound_uri'=>'http://www.conceptwiki.org/concept/' ,
'?ims_ocrs_compound_uri'=>'http://chemistry.openphacts.org/OPS' ,
'?ims_db_compound_uri'=>'http://bio2rdf.org/drugbank:',
'?ims_db_target_uri'=>'http://bio2rdf.org/drugbank',
'?ims_schembl_compound_uri' => 'http://rdf.ebi.ac.uk/resource/surechembl/molecule/',
'?ims_dg_gene_uri' => 'http://identifiers.org/ncbigene/',
'?ims_umls_disease_uri' => 'http://linkedlifedata.com/resource/umls/id/',
'?ims_omim_disease_uri' => 'http://identifiers.org/omim/',
);
var $expander_variables = array();//'?cw_uri' , '?ocrs_uri' , '?db_uri' , '?chembl_uri' , '?uniprot_uri' , '?aers_uri');
function __construct($request){
$this->_request = $request;
}
/**
* Called by SparqlWriter
*
* @return mixed|SimpleXMLElement[]
*/
function expandQuery ( $query , $input_uri, $lens ) {
$params='';
foreach ($this->expander_variables as &$var) {
if (strpos($query , $var) !== false) {
$params.= ", {$var}";
}
}
if ($params !='') {
$output = $this->expandQueryThroughExpander($query, $params, $input_uri, $lens);
}
else {
$output = $this->expandQueryThroughIMS($query, $input_uri, $lens);
}
return $output ;
}
private function getImsMapEndpoint() {
// return IMS_MAP_ENDPOINT;
$imsEndpointFromRequest = $this->_request->getParam('_imsendpoint');
if ($imsEndpointFromRequest) {
// logDebug("Using IMS endpoint from params: $imsEndpointFromRequest");
$imsMapEndpoint = $imsEndpointFromRequest . '/QueryExpander/mapUriRDF';
return $imsMapEndpoint;
} else if (IMS_MAP_ENDPOINT){
// logDebug("using IMS endpoint from environment variable: ".IMS_MAP_ENDPOINT);
$imsMapEndpoint = IMS_MAP_ENDPOINT;
return $imsMapEndpoint;
}else {
logDebug("No IMS endpoint was specified for <".$this->_request->getUri().">");
throw new ConfigGraphException("No IMS endpoint was specified for <".$this->_request->getUri().">");
}
}
private function expandQueryThroughIMS($query, $input_uri, $lens){
$output = $query ;
//build a hashtable which maps $variableName -> (uri, curl_handle, filter_clause)
$multiHandle = curl_multi_init();
$variableInfoMap = array();
//build curl multi handle setup
foreach ($this->IMS_variables AS $variableName => $pattern ){
if (strpos($query, $variableName)!==false) {
$variableInfoMap[$variableName] = array();
// $url = IMS_MAP_ENDPOINT;
$url = $this->getImsMapEndpoint();
$url .= '?rdfFormat=RDF/XML';
if ($pattern != '') {
$encoded_pattern = urlencode($pattern);
if (strpos($pattern, '&') !== FALSE) {
$encoded_pattern = str_replace('%26targetUriPattern%3D','&targetUriPattern=', $encoded_pattern);
}
$url .= '&targetUriPattern='.$encoded_pattern;
}
$url .= '&overridePredicateURI='.urlencode('http://www.w3.org/2004/02/skos/core#exactMatch');
$url .= '&lensUri=';
if ($lens==''){
$url .= 'Default';
}
else{
$url .= $lens;
}
$url .= '&Uri='.urlencode($input_uri);
logDebug("IMS Request (expandQueryThroughIMS):\n ".$url);
$variableInfoMap[$variableName]['url']=$url;
$ch = curl_init();
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
curl_setopt($ch,CURLOPT_HTTPHEADER,array ("Accept: text/plain"));
curl_setopt($ch, CURLOPT_URL, $url);
$variableInfoMap[$variableName]['handle'] = $ch;
curl_multi_add_handle($multiHandle, $ch);
}
}
$this->doSelectAndHandleResponses($multiHandle, $input_uri, $variableInfoMap);
curl_multi_close($multiHandle);
foreach ($variableInfoMap AS $variableName => $info){
if (isset($info['filter']) && preg_match("/(WHERE.*?)(GRAPH[^\}]*?\{[^\}]*?\\".$variableName.")/s",$output)) {
$output = preg_replace("/(WHERE.*?)(GRAPH[^\}]*?\{[^\}]*?\\".$variableName.")/s",
"$1 {$info['filter']} $2",$output, 1);
}
}
$output = preg_replace("/\*#\*/","}",$output);
return $output;
}
private function doSelectAndHandleResponses($multiHandle, $input_uri, &$variableInfoMap){
do{
do {
$mrc = curl_multi_exec($multiHandle, $activeHandles);
} while ($mrc==CURLM_CALL_MULTI_PERFORM);
if ($activeHandles==0 || $mrc!=CURLM_OK) break;
if (curl_multi_select($multiHandle) != -1){//wait for requests
// Disabled due to issue openphacts/OPS_LinkedDataApi#13
// The responses are handled later in foreach-handleResponse loop
//
// $this->handleAvailableResponses($multiHandle, $input_uri, $variableInfoMap);
}
}
while (true);
foreach ($variableInfoMap AS $variableName => $varInfo){
if (isset($varInfo['url'])&&!isset($varInfo['filter'])){
$this->handleResponse($varInfo, $multiHandle, $input_uri, $variableName, $variableInfoMap);
}
}
}
private function handleAvailableResponses($multiHandle, $input_uri, $variableInfoMap){
do{
$info = curl_multi_info_read($multiHandle);
if ($info===FALSE) break;
if ( $info['result'] != CURLE_OK ) {
logError("Error receiving info from the IMS");
break;
}
else{//process handle
foreach ($variableInfoMap AS $variableName => $varInfo){
if (isset($varInfo['handle']) && isset($info['handle']) && $varInfo['handle']==$info['handle']){
$this->handleResponse($varInfo, $multiHandle, $input_uri, $variableName, $variableInfoMap);
break;
}
}
}
}
while(true);
}
private function handleResponse($varInfo, $multiHandle, $input_uri, $variableName, &$variableInfoMap){
$response = curl_multi_getcontent($varInfo['handle']);
logDebug("IMS Response:\n{$response}");
curl_close($varInfo['handle']);
curl_multi_remove_handle($multiHandle, $varInfo['handle']);
//echo $url;
$graph = new SimpleGraph() ;
$graph->add_rdf($response);
$variableInfoMap[$variableName]['filter'] = $this->buildFilterFromMappings($graph, array($input_uri), $variableName);
}
private function expandQueryThroughExpander($query, $params, $input_uri, $lens){
$expanded = preg_replace("/\*#\*/","}",$query);
$url = IMS_EXPAND_ENDPOINT;
$url .= urlencode($expanded) ;
$params=substr($params, 2);
$url .= '¶meter=' ;
$url .= urlencode($params);
$url .= '&lensUri=';
if (empty($lens)){
$url .= 'Default';
}
else{
$url .= $lens;
}
$url .= '&inputURI=' . urlencode($input_uri) ;
$response = $this->getResponse($url, "application/xml");
logDebug("IMS Request (expandQueryThroughExpander):\n ".$url);
$expanded = simplexml_load_string($response)->expandedQuery ;
return $expanded;
}
/**
* 3 calls from SparqlWriter.getViewQueryForBatchUriList(...)
*
* @return mixed
*/
function expandBatchQuery( $query , $uriList, $lens) {
$rdf = "";
$output['expandedQuery']=$query;
$output['imsRDF']=$rdf;
foreach ($this->IMS_interm_variables AS $name => $pattern) {
if (strpos($query, $name)!==false){
$expanded = array();
// $urlStart = IMS_MAP_ENDPOINT;
$urlStart = $this->getImsMapEndpoint();
$urlStart .= '?rdfFormat=N-Triples';
if ($pattern != '') {
$encoded_pattern = urlencode($pattern);
if (strpos($pattern, '&') !== FALSE) {
$encoded_pattern = str_replace('%26targetUriPattern%3D','&targetUriPattern=', $encoded_pattern);
}
$urlStart .= '&targetUriPattern='.$encoded_pattern;
}
$urlStart .= '&overridePredicateURI='.urlencode('http://www.w3.org/2004/02/skos/core#exactMatch');
$urlStart .= '&lensUri=';
if ($lens==''){
$urlStart .= 'Default';
}
else{
$urlStart .= $lens;
}
$graph = new SimpleGraph() ;
$iter = 1;
$url=$urlStart;
foreach ($uriList AS $uri){
if ($iter % REQUEST_URI_NO == 0){
$response = $this->getResponse($url, "text/plain");
//echo $url . "\n";
$graph->add_rdf($response);
$rdf.=$response;
$url=$urlStart;
}
$url .= '&Uri='.urlencode($uri);
$iter++;
}
$response = $this->getResponse($url, "text/plain");
//echo $url . "\n";
$graph->add_rdf($response);
$rdf.=$response;
$filter = $this->buildFilterFromMappings($graph, $uriList, $name, $expanded);
if (isset($filter) ) {
$output['expandedQuery'] = preg_replace("/(WHERE.*?)(GRAPH[^\}]*?\{[^\}]*?\\".$name.")/s",
"$1{$filter} $2",
$output['expandedQuery']);
}
}
}
$output['imsRDF']=$rdf;
logDebug("IMS Request (expandBatchQuery) expandedQuery:\n " . $output['expandedQuery']);
logDebug("IMS Request (expandBatchQuery) imsRDF:\n " . $output['imsRDF']);
return $output;
}
private function buildFilterFromMappings($graph, $uriList, $variableName, &$expanded=array()){
logDebug('$uriList = ' . $uriList);
foreach ($uriList AS $input_uri){
foreach ($graph->get_subject_properties($input_uri, true) AS $p ) {
foreach($graph->get_subject_property_values($input_uri, $p) AS $mapping) {
$expanded[] = $mapping["value"];
}
}
}
if (count($expanded)>0){
$filter = " VALUES {$variableName} { ";
foreach (array_unique($expanded, SORT_STRING) AS $mapping) {
$filter.= "<{$mapping}> ";
}
$filter.= " }";
}
else{
$filter = " VALUES {$variableName} { <http://www.openphacts.org/api#no_mappings_found> }" ;
}
logDebug("FILTER clause: ". $filter);
return $filter;
}
private function getResponse($url, $mimetype){
$ch = curl_init($url);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
curl_setopt($ch,CURLOPT_HTTPHEADER,array ("Accept: ".$mimetype));
curl_setopt($ch,CURLOPT_FAILONERROR, true);
$response = curl_exec($ch);
curl_close($ch);
return $response;
}
}
?>