protected function execute(InputInterface $input, OutputInterface $output)
{
if ($input->getOption('remove-before')) {
$this->get('library.indexation')->deleteIndexes();
foreach (\LibraryDocumentCollectionPeer::doSelect(new \Criteria()) as $documentCollection) {
$this->get('library.documentCollection')->map($this->get('library.documentCollection')->export($documentCollection));
}
}
$vocabularyService = $this->get('library.vocabulary');
foreach ($this->get('library.documentCollection')->getList() as $documentCollection) {
$documents = $documentCollection->getLibraryDocuments();
if (count($documents)) {
$output->writeln($documentCollection->getName() . ':');
$progress = new ProgressBar($output, count($documents));
$progress->setFormat(' %current%/%max% [%bar%] %percent:3s%% %elapsed:6s%/%estimated:-6s%');
foreach ($documents as $document) {
$elasticaDocument = $this->get('library.indexation')->getDocument($document->getId());
if (false !== $elasticaDocument && !$input->getOption('update-image')) {
$this->get('library.indexation')->refreshDocument($document, $vocabularyService, false);
} else {
$this->get('library.indexation')->refreshDocument($document, $vocabularyService, !$input->getOption('ignore-image'));
}
$progress->advance();
}
$progress->finish();
$output->writeln("\n");
}
}
}
function importUMLSRelations( $umlsCollectionId, $relationCollectionContents, $query ) {
global
$db;
$queryResult = mysql_query( $query, $db );
$progressBar = new ProgressBar( mysql_num_rows( $queryResult ), 100 );
while ( $relation = mysql_fetch_row( $queryResult ) ) {
$relationType = $relation[2];
if ( strcmp( $relationType, 'CHD' ) == 0 ) {
$relationType = 'RN';
}
elseif ( strcmp( $relationType, 'PAR' ) == 0 ) {
$relationType = 'RB';
}
// echo "$definedMeaningId1 = $relation[0]\n";
$definedMeaningId1 = getDefinedMeaningFromCollection( $umlsCollectionId, $relation[0] );
$definedMeaningId2 = getDefinedMeaningFromCollection( $umlsCollectionId, $relation[1] );
$relationMeaningId = $relationCollectionContents[$relationType];
// echo "$definedMeaningId1 = $relation[0]\n";
// echo "$definedMeaningId1 = $relation[1]\n";
// echo "umlsCollectionId = $umlsCollectionId\n";
if ( !$definedMeaningId1 ) {
echo "Unknown cui $relation[0]\n";
print_r( $relation );
}
if ( !$definedMeaningId2 ) {
echo "Unknown cui $relation[1]\n";
print_r( $relation );
}
if ( !$relationMeaningId ) {
echo "Unknown relation $relationType\n";
print_r( $relationCollectionContents );
print_r( $relation );
}
if ( $definedMeaningId2 > 0 && $definedMeaningId1 > 0 && $relationMeaningId > 0 )
addRelation( $definedMeaningId2, $relationMeaningId, $definedMeaningId1 );
$progressBar->advance( 1 );
}
$progressBar->clear();
}
