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getExternalCore.php
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<?php
/**
* Author: Zuoshuang Xiang
* The University Of Michigan
* He Group
* Date: 2010-03-04
*
* This is the main program for processing user inputs, form queries,
* process query resuslt and output final results.
*/
set_time_limit(60*60);
include('inc/functions.php');
$vali=new Validation($_REQUEST);
$GALAXY_URL = $vali->getInput('GALAXY_URL', 'GALAXY_URL', 0, 100, true);
$num_queries = 0;
$outputURI = '';
$outputFile = 'import.owl';
$finalFile = createRandomPassword();
$str_inputs = array();
$array_ns = array();
//ontology original URIs
$array_original_ns = array();
$a_missing_term =array();
//SPARQL endpoint servers
$array_server = array();
$strQueryPrint = '';
$strSql= "select * from ontology where loaded='y'";
$db = ADONewConnection($driver);
$db->Connect($host, $username, $password, $database);
$rs = $db->Execute($strSql);
foreach($rs as $row) {
$array_ns[$row['ontology_abbrv']]=$row['ontology_graph_url'];
$array_original_ns[$row['ontology_abbrv']]=$row['ontology_url'];
$array_server[$row['ontology_abbrv']]=$row['end_point'];
}
//If user upload a file, parse the file and seperate into individual ontologies.
if (isset($_FILES['file']) && is_uploaded_file($_FILES['file']['tmp_name'])){
$data = trim(file_get_contents($_FILES['file']['tmp_name']));
file_put_contents("$userfiles/$finalFile.txt", $data);
$lines = preg_split('/[\r\n]+/', $data);
$str_input='';
$output_iri_next = false;
foreach($lines as $line) {
if (strpos($line, ' #')!==false) {
$line = trim(substr($line, 0, strpos($line, ' #')));
}
if (strpos($line, '#')===0 || trim($line)=='') {
//ignore comments or empty lines
}
elseif (strpos($line, '[Source ontology]')===0) {
if (strpos($str_input, '[Source ontology]')===0) {
$str_inputs[] = $str_input;
}
$str_input = '[Source ontology]';
}
elseif (strpos($line, '[URI of the OWL(RDF/XML) output file]')===0) {
$output_iri_next = true;
}
elseif ($line!='' && $output_iri_next == true) {
$outputURI = $line;
$output_iri_next = false;
}
else {
$str_input .= "\n" . $line;
}
if (strpos($line, '[')===0 && strpos($line, '[URI of the OWL(RDF/XML) output file]')===false) {
$output_iri_next = false;
}
}
if (strpos($str_input, '[Source ontology]')===0) {
$str_inputs[] = $str_input;
}
// print_r($str_inputs);
}
else {
$ontology= $vali->getInput('ontology', 'Ontology', 0, 128);
$ontology2 = $vali->getInput('ontology2', 'Your own ontology', 0, 1024);
$ontology = trim($ontology . "\n" . $ontology2);
$term_iris = $vali->getInput('term_iris', 'Lower level term IRIs to be imported', 10, 81920);
$top_term_iris = $vali->getInput('top_term_iris', 'Top level term IRIs to be imported', 0, 8192);
$retrieval_setting = $vali->getInput('retrieval_setting', 'Source term retrieval setting', 0, 128);
$outputURI = $vali->getInput('output_iri', 'URI of the OWL(RDF/XML) output file', 0, 128);
$annotation_iris = $vali->getInput('annotation_iris', 'annotation IRIs to be included', 0, 8192);
$excluding_annotation_iris = $vali->getInput('excluding_annotation_iris', 'annotation IRIs to be excluded', 0, 8192);
$str_inputs[] = "[URI of the OWL(RDF/XML) output file]
$outputURI
[Source ontology]
$ontology
[Low level source term URIs]
$term_iris
[Top level source term URIs and target direct superclass URIs]
$top_term_iris
[Source term retrieval setting]
$retrieval_setting
[Source annotation URIs]
$annotation_iris
[Source annotation URIs to be excluded]
$excluding_annotation_iris";
file_put_contents("$userfiles/$finalFile.txt", $str_inputs[0]);
}
$fileNames=array();
foreach ($str_inputs as $str_input) {
// print_r("<!--$str_input-->");
$section_values['ontology']='';
$section_values['term_iris']='';
$section_values['signature_term_iris']='';
$section_values['top_term_iris']='';
$section_values['retrieval_setting']='';
$section_values['annotation_iris']='';
$section_values['excluding_annotation_iris']='';
$lines = preg_split('/[\r\n]+/', $str_input);
$current_tag = '';
foreach ($lines as $line) {
$line = trim($line);
if (strpos($line, '[')===0) {
foreach($section_tags as $section_tag_var => $section_tag_txt){
if (strpos($line, $section_tag_txt)===0) {
$current_tag = $section_tag_var;
$section_values[$current_tag]='';
}
}
}
elseif (strpos($line, '#')===0) {
//ignore comments
}
else {
if (strpos($line, ' #')!==false) {
$line = trim(substr($line, 0, strpos($line, ' #')));
}
if ($current_tag!='' && $line!='') {
$section_values[$current_tag].=$line."\n";
}
}
}
$ontology = $section_values['ontology'];
$term_iris = $section_values['term_iris'];
$signature_term_iris = $section_values['signature_term_iris'];
$top_term_iris = $section_values['top_term_iris'];
$retrieval_setting = $section_values['retrieval_setting'];
$annotation_iris = $section_values['annotation_iris'];
$excluding_annotation_iris = $section_values['excluding_annotation_iris'];
if (strlen($term_iris)<10) {
$vali->concatError("At least one lower level term IRI is required.");
}
if (!isset($ontology) || strlen($ontology)<2) {
$vali->concatError("Ontology is required.");
}
// print("<!--$ontology-->");
//Get source ontology
if ($vali->getErrorMsg()=='') {
//parse ontology
$lines = preg_split('/[\r\n]+/', trim($ontology));
$ontology_uri = '';
$ontology_original_uri='';
$server_endpoint = '';
foreach ($lines as $line) {
$line = trim($line);
if (strpos($line, '#')===0) {
//ignore comments
}
else {
if (strpos($line, ' #')!==false) {
$line = trim(substr($line, 0, strpos($line, ' #')));
}
if (strpos($line, 'fromEndpoint ')===false) {
$ontology = $line;
if (isset($array_ns[$line])) {
$ontology_uri = $array_ns[$line];
$ontology_original_uri = $array_original_ns[$line];
$server_endpoint = $array_server[$line];
}
else {
$ontology_uri = $line;
$ontology_original_uri= $line;
}
}
else {
$line = trim(str_replace('fromEndpoint ', '', $line));
$server_endpoint = $line;
}
}
}
$retrieval_setting = isset($retrieval_setting) ? trim($retrieval_setting) : '';
if ($retrieval_setting=='') {
$retrieval_setting='includeNoIntermediates';
}
$outputNSs = array();
$outputNSs['http://www.w3.org/1999/02/22-rdf-syntax-ns#'] = 'rdf';
$outputNSs['http://www.w3.org/2002/07/owl#'] = 'owl';
$outputNSs['http://purl.obolibrary.org/obo/'] = 'obo';
$outputNSs['http://www.w3.org/2000/01/rdf-schema#'] = 'rdfs';
$strOutput='>
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
<rdfs:label xml:lang="en">imported from</rdfs:label>
</owl:AnnotationProperty>
';
$ns_rdf = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#';
$ns_rdfs = 'http://www.w3.org/2000/01/rdf-schema#';
$ns_owl = 'http://www.w3.org/2002/07/owl#';
$unprocessed_iris = array();
$processed_iris = array();
$parent_included_iris = array();
$terms_to_keep = array();
$top_term_iris=trim($top_term_iris);
//By default, don't retrive structure.
if ($top_term_iris=='') {
$top_term_iris = str_replace('includeAllChildren', '', $term_iris);
}
$a_parent_axoim=array();
//add top level source terms
$lines = preg_split('/[\r\n]+/', trim($top_term_iris));
$current_iri ='';
foreach ($lines as $line) {
$line = trim($line);
if (strpos($line, '#')===0) {
//ignore comments
}
else {
if (strpos($line, ' #')!==false) {
$line = trim(substr($line, 0, strpos($line, ' #')));
}
if (strpos($line, 'subClassOf ')===0) {
$line = trim(str_replace('subClassOf ', '', $line));
if ($current_iri!='') {
$terms_to_keep[$line] = 1;
$a_parent_axoim[$current_iri]="
<rdf:Description rdf:about=\"$current_iri\">
<rdfs:subClassOf rdf:resource=\"$line\"/>
</rdf:Description>
";
}
}
elseif (strpos($line, 'subPropertyOf ')===0) {
$line = trim(str_replace('subPropertyOf ', '', $line));
if ($current_iri!='') {
$terms_to_keep[$line] = 1;
$a_parent_axoim[$current_iri]="
<rdf:Description rdf:about=\"$current_iri\">
<rdfs:subPropertyOf rdf:resource=\"$line\"/>
</rdf:Description>
";
}
}
else {
$parent_included_iris[$line] = 'NA';
$unprocessed_iris[$line] = 'NA';
$current_iri=$line;
$terms_to_keep[$line] = 1;
}
}
}
//Get annotation URLs user wish to include
$annotation_iris_to_include = array();
$annotation_iris_to_include['http://www.w3.org/1999/02/22-rdf-syntax-ns#type'] = array('action'=>'', 'iri'=>'');
$annotation_iris_to_include['http://www.w3.org/2000/01/rdf-schema#subClassOf'] = array('action'=>'', 'iri'=>'');
$annotation_iris_to_include['http://www.w3.org/2000/01/rdf-schema#subPropertyOf'] = array('action'=>'', 'iri'=>'');
// $annotation_iris_to_include['http://www.w3.org/2002/07/owl#equivalentClass'] = array('action'=>'', 'iri'=>'');
$includeAllAxioms=false;
$includeAllAnnotationProperties=false;
$includeAllAxiomsRecursively=false;
if ($annotation_iris!='') {
$lines = preg_split('/[\r\n]+/', trim($annotation_iris));
$current_iri ='';
foreach ($lines as $line) {
$line = trim($line);
if (strpos($line, '#')===0) {
//ignore comments
}
else {
if (strpos($line, ' #')!==false) {
$line = trim(substr($line, 0, strpos($line, ' #')));
}
//get all Axioms
if ($line=='includeAllAxioms') {
$includeAllAxioms=true;
break;
}
//get all Axioms
if ($line=='includeAllAnnotationProperties') {
$includeAllAnnotationProperties=true;
break;
}
//get all Axioms recusively
if ($line=='includeAllAxiomsRecursively') {
$includeAllAxiomsRecursively=true;
break;
}
if(strpos($line, 'copyTo ')!==false) {
$line = trim(str_replace('copyTo ', '', $line));
$annotation_iris_to_include[$current_iri] = array('action'=>'copyTo', 'iri'=>$line);
$strOutput.=" <owl:AnnotationProperty rdf:about=\"$line\"/>\n";
}
elseif(strpos($line, 'mapTo ')!==false) {
$line = trim(str_replace('mapTo ', '', $line));
$annotation_iris_to_include[$current_iri] = array('action'=>'mapTo', 'iri'=>$line);
$strOutput.=" <owl:AnnotationProperty rdf:about=\"$line\"/>\n";
}
else {
$annotation_iris_to_include[$line] = array('action'=>'', 'iri'=>'');
$current_iri= $line;
}
}
}
}
$annotation_iris_to_exclude=array();
if (trim($excluding_annotation_iris)!='') {
$annotation_iris_to_exclude = preg_split('/[\r\n]+/', trim($excluding_annotation_iris));
}
//print_r($parent_included_iris);
//process term URIs to be imported and get super classes/properties.
$lines = preg_split('/[\r\n]+/', trim($term_iris));
$a_term_include_children=array();
$current_iri ='';
foreach ($lines as $line) {
if (strpos($line, '#')===0) {
//ignore comments
}
else {
if (strpos($line, ' #')!==false) {
$line = trim(substr($line, 0, strpos($line, ' #')));
}
if (strpos($line, 'includeAllChildren')===0) {
$a_term_include_children[$current_iri]=1;
}
else {
$import_term=trim($line);
$current_iri=$import_term;
$terms_to_keep[$import_term] =1;
if (!isset($processed_iris[$import_term])) {
$results = array($import_term => 'NA');
if (!isset($parent_included_iris[$import_term])) {
$unprocessed_iris[$import_term] = 'NA';
$querystring = "
PREFIX rdf: <$ns_rdf>
PREFIX rdfs: <$ns_rdfs>
PREFIX owl: <$ns_owl>
SELECT distinct ?s
FROM <$ontology_uri>
WHERE
{
{
SELECT ?s ?o
WHERE
{
{
?o rdfs:subClassOf ?s
}
UNION
{
?o owl:equivalentClass ?s1 .
?s1 owl:intersectionOf ?s2 .
?s2 rdf:first ?s
}
UNION
{
?o rdfs:subPropertyOf ?s
}
UNION
{
?o owl:equivalentProperty ?s1 .
?s1 owl:intersectionOf ?s2 .
?s2 rdf:first ?s
}
}
} OPTION (TRANSITIVE, t_in(?o), t_out(?s)).
FILTER (?o= <$import_term>)
}";
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$tmp_results = json_query($querystring, $server_endpoint);
//print("\n\n<!--\n$querystring-->\n\n");
// print_r($tmp_results);
$num_queries++;
foreach($tmp_results as $tmp_result) {
$tmp_iri = $tmp_result['s'];
if(!isset($processed_iris[$tmp_iri]) && !isset($parent_included_iris[$tmp_iri])) {
$unprocessed_iris[$tmp_iri] = '';
}
else {
break;
}
}
}
else {
if (!isset($processed_iris[$import_term])) {
$unprocessed_iris[$import_term] = '';
}
}
}
}
}
}
$querystring = "SELECT DISTINCT ?s
FROM <$ontology_uri>
WHERE {
?s ?p ?o.
FILTER (?s in (<http://null>, <". join(">
, <", array_keys($terms_to_keep)) .">))
}
";
$querystring = formatQuerySelect($querystring);
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$a_existing_term = json_query($querystring, $server_endpoint);
$a_missing_term = array_merge($a_missing_term, $terms_to_keep);
if (!empty($a_existing_term)) {
foreach ($a_existing_term as $existing_term) {
if (isset($a_missing_term[$existing_term['s']])) unset($a_missing_term[$existing_term['s']]);
}
}
//Retrieve children terms
if (!empty($a_term_include_children)) {
foreach ($a_term_include_children as $import_term=>$tmpLabel) {
$terms_to_keep[$import_term] =1;
if (!isset($processed_iris[$import_term])) {
$results = array($import_term => 'NA');
$querystring="
PREFIX rdf: <$ns_rdf>
PREFIX rdfs: <$ns_rdfs>
PREFIX owl: <$ns_owl>
SELECT distinct ?o
FROM <$ontology_uri>
WHERE
{
{
SELECT ?s ?o
WHERE
{
{
?o rdfs:subClassOf ?s
}
UNION
{
?o owl:equivalentClass ?s1 .
?s1 owl:intersectionOf ?s2 .
?s2 rdf:first ?s
}
UNION
{
?o rdfs:subPropertyOf ?s
}
UNION
{
?o owl:equivalentProperty ?s1 .
?s1 owl:intersectionOf ?s2 .
?s2 rdf:first ?s
}
}
} OPTION (TRANSITIVE, t_in(?s), t_out(?o)).
FILTER (?s= <$import_term>)
}";
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$tmp_results = json_query($querystring, $server_endpoint);
//print("\n\n<!--\n$querystring-->\n\n");
$num_queries++;
foreach($tmp_results as $tmp_result) {
$unprocessed_iris[$tmp_result['o']]='';
$terms_to_keep[$tmp_result['o']] =1;
}
}
}
}
$related_terms=array();
$loop_num=0;
//Send query to servers and process response.
/* 2017/02/23: Update to support Virtuoso 7 */
$prefix_count = 1;
/* End 2017/02/23 */
while (!empty($unprocessed_iris)) {
$loop_num++;
if ($loop_num>10000) {
print("Dead loop???");
exit();
}
$tmp_unprocessed_iris=array();
$rdf='';
if ($includeAllAxioms || $includeAllAxiomsRecursively) {
$querystring = "
DEFINE sql:describe-mode \"CBD\"
DESCRIBE <".join('>
<', array_keys($unprocessed_iris)).">
FROM <$ontology_uri>";
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$fields = array();
$fields['default-graph-uri'] = $ontology_uri;
$fields['format'] = 'application/rdf+xml';
$fields['debug'] = 'on';
$fields['query'] = $querystring;
// print("<!--$querystring-->\n");
$rdf .= curl_post_contents($server_endpoint, $fields);
}
else {
if ($includeAllAnnotationProperties) {
$querystring = "
CONSTRUCT {?s ?p ?o}
FROM <$ontology_uri>
WHERE {
{?s ?p ?o.
?p <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#AnnotationProperty>.
FILTER (?s in (<".join('>
, <', array_keys($unprocessed_iris)).">))
}
UNION
{?s ?p ?o.
FILTER (?p in (<http://www.w3.org/2000/01/rdf-schema#label>)).
FILTER (?s in (<".join('>
, <', array_keys($unprocessed_iris)).">))
}
}
";
$querystring = formatQuery($querystring);
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$fields = array();
$fields['default-graph-uri'] = $ontology_uri;
$fields['format'] = 'application/rdf+xml';
$fields['debug'] = 'on';
$fields['query'] = $querystring;
// print("<!--$querystring-->\n");
$rdf .= curl_post_contents($server_endpoint, $fields);
}
foreach ($annotation_iris_to_include as $annotation_iri => $mapping) {
if ($mapping['action']=='copyTo') {
$querystring = "
CONSTRUCT {
?s <$annotation_iri> ?o.
?s <{$mapping['iri']}> ?o
}
FROM <$ontology_uri>
WHERE {?s <$annotation_iri> ?o.
FILTER (?s in (<".join('>
, <', array_keys($unprocessed_iris)).">))
}
";
}
elseif ($mapping['action']=='mapTo') {
$querystring = "
CONSTRUCT {
?s <{$mapping['iri']}> ?o.
?s <{$mapping['iri']}> ?o2
}
FROM <$ontology_uri>
WHERE {
{?s <$annotation_iri> ?oa .
?oa <http://www.w3.org/2000/01/rdf-schema#label> ?o.
FILTER (?s in (<".join('>
, <', array_keys($unprocessed_iris)).">))
}
UNION
{?s <$annotation_iri> ?o2.
FILTER (isLiteral(?o2)).
FILTER (?s in (<".join('>
, <', array_keys($unprocessed_iris)).">))
}
}
";
}
else {
$querystring = "
CONSTRUCT {
?s <$annotation_iri> ?o
}
FROM <$ontology_uri>
WHERE {
?s <$annotation_iri> ?o.
FILTER (?s in (<".join('>
, <', array_keys($unprocessed_iris)).">))
}
";
}
$querystring = formatQuery($querystring);
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$fields = array();
$fields['default-graph-uri'] = $ontology_uri;
$fields['format'] = 'application/rdf+xml';
$fields['debug'] = 'on';
$fields['query'] = $querystring;
// print("<!--$querystring-->\n");
$rdf .= curl_post_contents($server_endpoint, $fields);
}
}
foreach ($unprocessed_iris as $tmp_iri => $label) {
$processed_iris[$tmp_iri] = $label;
}
/* 2017/02/23: Update to support Virtuoso 7 */
// print_r( $rdf );
$rdfs = preg_split( '/<\?xml[^\?]*\?>/', $rdf );
foreach ( $rdfs as $rdf ) {
# Extract xmlns
$xmlns = [];
if ( preg_match_all( '/xmlns:(\w+)="([^"]+?)"/', $rdf, $matches ) ) {
foreach ( $matches[0] as $i => $full_match ) {
if ( !array_key_exists( $matches[1][$i], $xmlns ) ) {
$xmlns[$matches[1][$i]] = $matches[2][$i];
}
if ( !array_key_exists( $matches[2][$i], $outputNSs ) ) {
$tmp_split = preg_split( '/[\/#]/', $matches[2][$i] );
$tmp_ns = array_pop( $tmp_split );
if ( $tmp_ns == '' or array_search( $tmp_ns, $outputNSs ) ) {
$tmp_ns = array_pop( $tmp_split );
}
if ( preg_match( '/[^\w\d]/', $tmp_ns ) ) {
$tmp_ns = "ns$prefix_count";
$prefix_count = $prefix_count + 1;
}
$outputNSs[$matches[2][$i]] = $tmp_ns;
}
}
}
# Process descriptions
if ( preg_match_all( '/(<rdf:Description[\s\S]*?(?=(rdf:Description>)))/', $rdf, $matches ) ) {
foreach( $matches[0] as $match ) {
$lines = preg_split( '/\n/', $match );
$first_line = array_shift( $lines );
preg_match_all( '/rdf:about="([^"]*)"/', $first_line, $tmp_matches );
$current_iri = $tmp_matches[1][0];
array_pop( $lines );
# Remove subClassOf/subPropertyOf/ axioms for parent terms
foreach ( $parent_included_iris as $parent_included_iri => $parent_included_label ) {
if ( $parent_included_iri == $current_iri ) {
foreach ( $lines as $i => $line ) {
if ( isset( $lines[$i] ) && strpos( $line, "rdfs:subClassOf" ) !== false ) {
unset( $lines[$i] );
break;
}
if ( isset( $lines[$i] ) && strpos( $line, "rdfs:subPropertyOf" ) !== false ) {
unset( $lines[$i] );
break;
}
}
}
}
foreach ( $lines as $i => $line ) {
# Remove axioms if not includeAllAxioms or includeAllAxiomsRecursively
if ( !$includeAllAxioms && !$includeAllAxiomsRecursively ) {
if ( isset( $lines[$i] ) && strpos( $line, "rdfs:subClassOf rdf:nodeID=" ) !== false ) {
unset( $lines[$i] );
}
if ( isset( $lines[$i] ) && strpos( $line, "rdfs:subPropertyOf rdf:nodeID=" ) !== false ) {
unset( $lines[$i] );
}
}
# Remove disjointWith
if ( isset( $lines[$i] ) && strpos( $line, "disjointWith" ) !== false ) {
unset( $lines[$i] );
}
# Remove owl:Thing
if ( isset( $lines[$i] ) && strpos( $line, '<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>' ) ) {
unset( $lines[$i] );
}
# Check for unprocessed iris
if ( isset( $lines[$i] ) && preg_match( '/<(\w+?):(\w+)/', $line, $tmp_match) ) {
$tmp_iri = $xmlns[$tmp_match[1]] . $tmp_match[2];
if ( !isset( $processed_iris[$tmp_iri] ) ) {
$tmp_unprocessed_iris[$tmp_iri] = 'NA';
}
}
# Reformat namespace
if ( isset( $lines[$i] ) && preg_match( '/<(\w+?):(\w+)/', $line, $tmp_match) ) {
if ( !array_search( $tmp_match[1], $outputNSs ) ) {
$lines[$i] = str_replace( $tmp_match[1], $outputNSs[$xmlns[$tmp_match[1]]], $line );
}
}
if ( isset( $lines[$i] ) && preg_match( '/<\/(\w+?):(\w+)/', $line, $tmp_match) ) {
if ( !array_search( $tmp_match[1], $outputNSs ) ) {
$lines[$i] = str_replace( $tmp_match[1], $outputNSs[$xmlns[$tmp_match[1]]], $line );
}
}
# For backward-compatibility with Virtuoso version 6.2.1
# Fix for "n0pred" beening used for different xmlnss
if ( isset( $lines[$i] ) && strpos( $line, '<n0pred:' ) !== false ) {
preg_match( '/xmlns:n0pred="(\S+)"/', $line, $tmp_matches );
$NSTmp = $tmp_matches[1];
if ( array_key_exists( $NSTmp, $outputNSs ) ) {
$prefixTmp = $outputNSs[$NSTmp];
} else {
$tokens = preg_split( '/\//', trim( $NSTmp ) );
$prefixTmp = preg_replace( '/[[:^alnum:]]/', '', array_pop( $tokens ) );
if ( preg_match( '/^\d+$/', $prefixTmp ) ) {
$prefixTmp = preg_replace( '/[[:^alnum:]]/', '', array_pop( $tokens ) . $prefixTmp );
}
$prefixTmp = 'p_' . $prefixTmp;
if ( in_array( $prefixTmp, $outputNSs ) ) {
$j = 1;
while ( in_array( $prefixTmp . $j, $outputNSs ) ) {
$j++;
}
$prefixTmp .= $j;
}
}
$outputNSs[$NSTmp] = $prefixTmp;
$lines[$i] = str_replace( 'n0pred:', $prefixTmp . ':', $line );
$lines[$i] = preg_replace( '/xmlns:n0pred="(\S+)"/', '', $line );
}
# Add 'imported_from' annotation
if ( isset( $lines[$i] ) && preg_match( '/<rdf:type rdf:resource="http:\/\/www\.w3\.org\/2002\/07\/owl#Class"/', $line ) ) {
$lines[] = "<obo:IAO_0000412 rdf:resource=\"$ontology_original_uri\"/>";
}
if ( isset( $lines[$i] ) && preg_match( '/<rdf:type rdf:resource="http:\/\/www\.w3\.org\/2002\/07\/owl#ObjectProperty"/', $line ) ) {
$lines[] = "<obo:IAO_0000412 rdf:resource=\"$ontology_original_uri\"/>";
}
if ( isset( $lines[$i] ) && preg_match( '/<rdf:type rdf:resource="http:\/\/www\.w3\.org\/2002\/07\/owl#DatatypeProperty"/', $line ) ) {
$lines[] = "<obo:IAO_0000412 rdf:resource=\"$ontology_original_uri\"/>";
}
}
# Store processed output
if ( !empty( $lines ) ) {
$output = join( PHP_EOL, $lines );
$strOutput .= $first_line . PHP_EOL . $output . PHP_EOL . "</rdf:Description>";
}
# Extract unprocessed axioms for includeAllAxiomsRecursively
if ( $includeAllAxiomsRecursively ) {
preg_match_all( '/resource="(.+?)"/', $output, $tmp_matches );
foreach ( $tmp_matches[1] as $tmp_match ) {
if ( !isset( $processed_iris[$tmp_match] ) && !isset( $included_iris[$tmp_match] ) ) {
$tmp_unprocessed_iris[$tmp_match] = 'NA';
}
}
}
# Extract labels and types for related terms
if ( $includeAllAxioms ) {
preg_match_all( '/resource="(.+?)"/', $output, $tmp_matches );
foreach ( $tmp_matches[1] as $tmp_match ) {
if ( !isset( $processed_iris[$tmp_match] ) && !isset( $included_iris[$tmp_match] ) ) {
$related_terms[$tmp_match] = 'NA';
}
}
}
}
}
}
/* End 2017/02/23 */
$unprocessed_iris = $tmp_unprocessed_iris;
}
// print_r( $related_terms );
//retrieve label & type for related terms.
if (!empty($related_terms)) {
$querystring = "
PREFIX rdf: <$ns_rdf>
PREFIX rdfs: <$ns_rdfs>
PREFIX owl: <$ns_owl>
CONSTRUCT {
?s rdf:type ?o
}
FROM <$ontology_uri>
WHERE {
?s rdf:type ?o.
FILTER (?s in (<".join('>
, <', array_keys($related_terms)).">))
}
";
$querystring = formatQuery($querystring);
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$fields = array();
$fields['default-graph-uri'] = $ontology_uri;
$fields['format'] = 'application/rdf+xml';
$fields['debug'] = 'on';
$fields['query'] = $querystring;
$rdf = curl_post_contents($server_endpoint, $fields);
/* 2017/02/23: Update to support Virtuoso 7 */
if ( preg_match_all( '/(<rdf:Description[\s\S]*?(?=(<\/rdf:Description>)))/', $rdf, $matches ) ){
foreach ( $matches[0] as $i => $match ) {
$strOutput .= PHP_EOL . $matches[1][$i] . $matches[2][$i] . PHP_EOL;
}
}
/* End 2017/02/23 */
$querystring = "
PREFIX rdf: <$ns_rdf>
PREFIX rdfs: <$ns_rdfs>
PREFIX owl: <$ns_owl>
CONSTRUCT {
?s rdfs:label ?o
}
FROM <$ontology_uri>
WHERE {
?s rdfs:label ?o.
FILTER (?s in (<".join('>
, <', array_keys($related_terms)).">))
}
";
$querystring = formatQuery($querystring);
$strQueryPrint .= $querystring . "\n\n====================================================================\n\n";
$fields = array();
$fields['default-graph-uri'] = $ontology_uri;
$fields['format'] = 'application/rdf+xml';
$fields['debug'] = 'on';
$fields['query'] = $querystring;
$rdf = curl_post_contents($server_endpoint, $fields);
/* 2017/02/23: Update to support Virtuoso 7 */
if ( preg_match_all( '/(<rdf:Description[\s\S]*?(?=(<\/rdf:Description>)))/', $rdf, $matches ) ){
foreach ( $matches[0] as $i => $match ) {
$strOutput .= PHP_EOL . $matches[1][$i] . $matches[2][$i] . PHP_EOL;
}
}
/* End 2017/02/23 */
}
if (empty($fileNames) && sizeof($str_inputs)==1) {
$fileName=$finalFile;
}
else {
$fileName=createRandomPassword();
}
$tmpOutputURI="http://ontofox.hegroup.org/$fileName.owl";
if (empty($fileNames) && $outputURI!='' && sizeof($str_inputs)==1) {
$tmpOutputURI = $outputURI;
}
foreach($a_parent_axoim as $tmp_c_iri=>$tmp_p_output) {
if (!isset($a_missing_term[$tmp_c_iri])) {
$strOutput.=$tmp_p_output;
}
}
$strOutput .= "
<owl:Ontology rdf:about=\"$tmpOutputURI\"/>
</rdf:RDF>";
$strOutput = preg_replace('/<rdf:Description rdf:about="(\S+)"><rdf:type rdf:resource="http:\/\/www.w3.org\/2002\/07\/owl#ObjectProperty"\/><\/rdf:Description>/', "<owl:ObjectProperty rdf:about=\"$1\"/>", $strOutput);
foreach ($outputNSs as $NSTmp => $prefixTmp) {
$strOutput = "
xmlns:$prefixTmp=\"$NSTmp\"" . $strOutput;
}
$strOutput = '<?xml version="1.0" encoding="utf-8" ?>