public function add_rel($params)
{
$res = addRelation($params["id"], $params["child_id"], $params["rel_id"]);
$this->logPerson($params, 2);
return $res;
}
foreach (['children', 'parents', 'tokens', 'children_to_parents'] as $table) {
$query = $db->createQueryBuilder();
$query->delete($table)->execute();
// $db->fetchAll('DELETE FROM ' . $table );
}
//$db->delete('children', []);
//$db->delete('parents', []);
//$db->delete('tokens', []);
//$db->delete('children_to_parents', []);
$childrens = [Children::createObj(['name' => 'Children' . uniqid()]), Children::createObj(['name' => 'TestChildren']), Children::createObj(['name' => 'Children' . uniqid()]), Children::createObj(['name' => 'Children' . uniqid()]), Children::createObj(['name' => 'Children' . uniqid()])];
saveAll($childrens);
$parents = [Parents::createObj(['login' => 'Parent' . uniqid(), 'password' => uniqid()]), Parents::createObj(['login' => 'TestParent', 'password' => 'ParentPass']), Parents::createObj(['login' => 'Parent' . uniqid(), 'password' => uniqid()]), Parents::createObj(['login' => 'Parent' . uniqid(), 'password' => uniqid()])];
saveAll($parents);
$tokens = addTokens($parents);
saveAll($tokens);
addRelation($parents, $childrens);
function addTokens($parents)
{
$tokens = [];
foreach ($parents as $parent) {
$tokens[] = Tokens::createObj(['parent_id' => $parent->id, 'token' => uniqid('token-'), 'type' => rand(0, 1)]);
}
return $tokens;
}
function saveAll(array $collection)
{
foreach ($collection as $el) {
$el->save();
}
}
function addRelation(array $parents, array $childrens)
function flushProperRelations(&$relationsArr, &$conceptsArr, &$verb, &$lastSubject, $ssPoSPattern, &$filledConcepts)
{
if (count($conceptsArr) >= 2) {
if (empty($verb)) {
$verb = "n/a";
}
if ($conceptsArr[0] != $conceptsArr[1]) {
$type = "NON-TAXONOMIC";
addRelation($relationsArr, $type, $conceptsArr[0], $verb, $conceptsArr[1], $ssPoSPattern);
if (count($conceptsArr) > 2) {
addRelation($relationsArr, $type, $conceptsArr[1], "n/a", $conceptsArr[2], $ssPoSPattern);
addRelation($relationsArr, $type, $conceptsArr[0], "n/a", $conceptsArr[2], $ssPoSPattern);
}
}
$conceptsArr = array();
$verb = null;
$filledConcepts = 0;
}
if (count($conceptsArr) == 1 && !empty($verb) && !empty($lastSubject) && $conceptsArr[0] != $lastSubject) {
//echoN("||||".$conceptsArr[0]."|".$lastSubject);
$temp = $conceptsArr[0];
$conceptsArr[0] = $lastSubject;
$conceptsArr[1] = $temp;
// many problems
if ($conceptsArr[0] != $conceptsArr[1]) {
$type = "NON-TAXONOMIC";
addRelation($relationsArr, $type, $conceptsArr[0], $verb, $conceptsArr[1], $ssPoSPattern);
}
$conceptsArr = array();
$verb = null;
$filledConcepts = 0;
}
}
function rollBackRelation( $rollBackAction, $relationId, $firstMeaningId, $relationTypeId, $secondMeaningId, $operation ) {
if ( shouldRemove( $rollBackAction, $operation ) ) {
removeRelationWithId( $relationId );
}
elseif ( shouldRestore( $rollBackAction, $operation ) ) {
addRelation( $firstMeaningId, $relationTypeId, $secondMeaningId );
}
}
public function add( IdStack $idPath, $record ) {
$objectId = $this->objectIdFetcher->fetch( $idPath->getKeyStack() );
$definedMeaningAttributeId = $this->determineAttributeId( $idPath, "DM", $record->relationType );
$definedMeaningValue = $record->otherDefinedMeaning;
if ( $definedMeaningAttributeId != 0 && $definedMeaningValue != 0 ) {
addRelation( $objectId, $definedMeaningAttributeId, $definedMeaningValue );
}
}
public function addEntry( SwissProtEntry $entry, $proteinMeaningId, $organismSpecificGene, $organismSpeciesMeaningId ) {
$definedMeaningId = $this->addOrganismSpecificProtein( $entry->protein->name, $entry->organism, $proteinMeaningId, $organismSpecificGene, $organismSpeciesMeaningId );
// change name to make sure it works in wiki-urls:
$swissProtExpression = str_replace( '_', '-', $entry->name );
addSynonymOrTranslation( $swissProtExpression, $this->languageId, $definedMeaningId, true );
foreach ( $entry->protein->synonyms as $key => $synonym )
addSynonymOrTranslation( $synonym, $this->languageId, $definedMeaningId, true );
addDefinedMeaningToCollection( $definedMeaningId, $this->collectionId, $entry->accession );
// add the comment fields as text attributes to the entry and link comments with
// the appropriate definedMeaning
$this->addComments( $entry, $definedMeaningId, $proteinMeaningId, $organismSpeciesMeaningId );
// add EC number:
if ( $entry->EC != "" ) {
$ECNumberMeaningId = $this->getOrCreateECNumberMeaningId( $entry->EC );
addRelation( $definedMeaningId, $this->activityConceptId, $ECNumberMeaningId );
}
// add keywords:
// foreach ($entry->keywords as $key => $keyword) {
// if (array_key_exists($keyword, $this->keyword2GoMeaningIdMapping)) {
// $goMeaningId = $this->keyword2GoMeaningIdMapping[$keyword];
// addRelation($definedMeaningId, $this->keywordConceptId, $goMeaningId);
// }
// }
foreach ( $entry->GOReference as $key => $goReference ) {
$relationConcept = 0;
switch( $goReference->type ) {
case "biological process":
$relationConcept = $this->biologicalProcessConceptId;
break;
case "molecular function":
$relationConcept = $this->molecularFunctionConceptId;
break;
case "cellular component":
$relationConcept = $this->cellularComponentConceptId;
break;
}
if ( $relationConcept != 0 )
addRelation( $definedMeaningId, $relationConcept, $this->goCollection->getOrCreateMember( $goReference->goCode ) );
}
// Add 'included' functional domains:
foreach ( $entry->protein->domains as $key => $domain ) {
$domainMeaningId = $this->addFunctionalDomain( $domain );
foreach ( $domain->synonyms as $domainKey => $synonym )
addSynonymOrTranslation( $synonym, $this->languageId, $domainMeaningId, true );
addRelation( $definedMeaningId, $this->consistsOfId, $domainMeaningId );
}
// Add 'contained' proteins:
foreach ( $entry->protein->components as $key => $component ) {
$componentMeaningId = $this->addContainedProtein( $component, $entry->organism, $organismSpeciesMeaningId );
foreach ( $component->synonyms as $componentKey => $synonym )
addSynonymOrTranslation( $synonym, $this->languageId, $componentMeaningId, true );
addRelation( $definedMeaningId, $this->containsConceptId, $componentMeaningId );
}
return $definedMeaningId;
}
function importSemanticTypeRelations( $collectionId, $relationCollectionContents, $query ) {
global
$db;
$queryResult = mysql_query( $query, $db );
while ( $relation = mysql_fetch_row( $queryResult ) ) {
$relationType = $relation[1];
$definedMeaningId1 = getDefinedMeaningFromCollection( $collectionId, $relation[0] );
$definedMeaningId2 = getDefinedMeaningFromCollection( $collectionId, $relation[2] );
$relationMeaningId = $relationCollectionContents[$relationType];
if ( !$relationMeaningId ) {
echo "Unknown relation $relationType\n";
print_r( $relationCollectionContents );
print_r( $relation );
}
if ( !$definedMeaningId1 ) {
echo "Unknown semantic type $relation[0]\n";
print_r( $relation );
}
if ( !$definedMeaningId2 ) {
echo "Unknown semantic type $relation[2]\n";
print_r( $relation );
}
if ( $definedMeaningId2 > 0 && $definedMeaningId1 > 0 && $relationMeaningId > 0 )
addRelation( $definedMeaningId2, $relationMeaningId, $definedMeaningId1 );
}
}
if ($synonym != $parentConceptName) {
$enrichedFinalConcepts[$finalConceptName]['EXTRA']['AKA']['EN']['WORDNET'] = cleanWordnetCollocation($synonym);
}
}
} else {
//echoN("##$finalConceptName|T-BOX");
//echoN("$concept,$is_a_relation_name_ar,$finalConceptName");
/*
* WILL NOT DO IT HERE SINCE SOME RELATIONS ARE EXCLUDED LATER, SO OPERATIONS DONE HERE
* CAN'T BE REVERTED BACK, WILL BE MOVED AFTER EXCLUSION INSTEAD
*/
//$enrichedFinalConcepts[$finalConceptName]['CONCEPT_TYPE']='T-BOX';
}
echoN("XPP: 2 {$finalConceptName}");
$relationType = "TAXONOMIC";
$res = addRelation($relationsArr, $relationType, $concept, "{$is_a_relation_name_ar}", $finalConceptName, "{$is_a_relation_name_en}");
if ($res == true) {
$newRelationsAdded++;
}
}
}
}
}
//if ( $conceptsEnriched>3) break;
}
echoN("Concepts Enriched from (WORDNET):{$conceptsEnriched}");
echoN("New Concepts Added:{$newConceptsAdded}");
echoN("New Relations Added:{$newRelationsAdded}");
preprint_r($newConceptsAddedArr);
//preprint_r($enrichedFinalConcepts);exit;
file_put_contents("{$ONTOLOGY_EXTRACTION_FOLDER}/temp.final.concepts.stage6", serialize($enrichedFinalConcepts));
