function execute( $par ) {
global $wgOut, $wgUser, $wgRequest;
$wgOut->setPageTitle( 'Add Collection' );
if ( !$wgUser->isAllowed( 'addcollection' ) ) {
$wgOut->addHTML( 'You do not have permission to add a collection.' );
return false;
}
$dbr = wfGetDB( DB_MASTER );
if ( $wgRequest->getText( 'collection' ) ) {
require_once( 'WikiDataAPI.php' );
require_once( 'Transaction.php' );
$dc = $wgRequest->getText( 'dataset' );
$collectionName = $wgRequest->getText( 'collection' );
startNewTransaction( $wgUser->getID(), wfGetIP(), 'Add collection ' . $collectionName );
bootstrapCollection( $collectionName, $wgRequest->getText( 'language' ), $wgRequest->getText( 'type' ), $dc );
$wgOut->addHTML( wfMsg( 'ow_collection_added', $collectionName ) . "<br />" );
}
$datasets = wdGetDatasets();
$datasetarray[''] = wfMsgSc( "none_selected" );
foreach ( $datasets as $datasetid => $dataset ) {
$datasetarray[$datasetid] = $dataset->fetchName();
}
$wgOut->addHTML( getOptionPanel(
array(
'Collection name:' => getTextBox( 'collection' ),
'Language of name:' => getSuggest( 'language', 'language' ),
'Collection type:' => getSelect( 'type', array( '' => 'None', 'RELT' => 'RELT', 'LEVL' => 'LEVL', 'CLAS' => 'CLAS', 'MAPP' => 'MAPP' ) ),
'Dataset:' => getSelect( 'dataset', $datasetarray )
),
'', array( 'create' => wfMsg( 'ow_create' ) )
) );
}
$result = $dbr->query( "select user_id from user where user_name = '$userName'" );
if ( $row = $dbr->fetchObject( $result ) ) {
return $row->user_id;
}
else {
return - 1;
}
}
$userId = getUserId( 'Root' );
if ( $userId == - 1 ) {
echo "root user undefined\n";
die;
}
setUser( $userId );
$datasets = getDatasets();
$dbr = wfGetDB( DB_SLAVE );
foreach ( $datasets as $dataset ) {
foreach ( $datasets as $otherdataset ) {
if ( $dataset != $otherdataset ) {
echo "mapping between $otherdataset and $dataset\n";
setDefaultDC( $otherdataset );
startNewTransaction( $userId, wfGetIP(), 'Add collection ', $dataset );
bootstrapCollection( $dataset, '85', 'MAPP' );
}
}
}
?>
/** Write the dm to the correct collection for a particular dc */
function writeDmToCollection( $dc, $collid, $uuid, $dm_id, $override_transaction = null ) {
global
$wgUser;
// if(is_null($dc)) {
// $dc=wdGetDataSetContext();
// }
$dbw = & wfGetDB( DB_MASTER );
$collection_contents = "{$dc}_collection_contents";
$collid = $dbw->addQuotes( $collid );
$uuid = $dbw->addQuotes( $uuid );
$dm_id = $dbw->addQuotes( $dm_id );
$add_transaction_id = $override_transaction;
if ( is_null( $add_transaction_id ) ) {
startNewTransaction( $wgUser->getId(), wfGetIP(), "inserting collection $collid", $dc );
$add_transaction_id = getUpdateTransactionId();
}
$sql = "
INSERT INTO $collection_contents
SET collection_id=$collid,
internal_member_id=$uuid,
member_mid=$dm_id,
add_transaction_id=$add_transaction_id
";
$result = $dbw->query( $sql );
}
/** start a new copy transaction
* Gets a virtual user id from the wikidata_sets table, if available
* (else uses user 0)
* There's still some issues with transactions especially wrt with user assignment
* where we intersect with the (old) "WikiDataAPI".
*/
public static function newCopyTransaction( $dc1, $dc2 ) {
$datasets = CopyTools::getRow_noDC( "wikidata_sets", "WHERE set_prefix=\"$dc1\"" );
if ( $datasets == false ) {
throw new Exception( "Dataset info for $dc1 not found." );
}
if ( array_key_exists( "virtual_user_id", $datasets ) ) {
$virtual_user_id = $datasets["virtual_user_id"];
} else {
$virtual_user_id = 0;
}
# The id might exist, but still be null.
if ( is_null( $virtual_user_id ) ) {
$virtual_user_id = 0;
}
startNewTransaction(
$virtual_user_id,
"0.0.0.0",
"copying from $dc1 to $dc2",
$dc2 );
}
function rollBackTransactions( $recordSet ) {
$o = OmegaWikiAttributes::getInstance();
global
$wgRequest, $wgUser;
$summary = $wgRequest->getText( 'summary' );
startNewTransaction( $wgUser->getID(), wfGetIP(), $summary );
$idStack = new IdStack( 'transaction' );
$transactionKeyStructure = $recordSet->getKey();
for ( $i = 0; $i < $recordSet->getRecordCount(); $i++ ) {
$transactionRecord = $recordSet->getRecord( $i );
$transactionId = $transactionRecord->transactionId;
$idStack->pushKey( simpleRecord( $transactionKeyStructure, array( $transactionId ) ) );
$updatesInTransaction = $transactionRecord->updatesInTransaction;
$idStack->pushAttribute( $o->updatesInTransaction );
$updatedDefinitions = $updatesInTransaction->updatedDefinition;
$idStack->pushAttribute( $o->updatedDefinition );
rollBackDefinitions( $idStack, $updatedDefinitions );
$idStack->popAttribute();
$updatedRelations = $updatesInTransaction->updatedRelations;
$idStack->pushAttribute( $o->updatedRelations );
rollBackRelations( $idStack, $updatedRelations );
$idStack->popAttribute();
$updatedClassMemberships = $updatesInTransaction->updatedClassMembership;
$idStack->pushAttribute( $o->updatedClassMembership );
rollBackClassMemberships( $idStack, $updatedClassMemberships );
$idStack->popAttribute();
$updatedClassAttributes = $updatesInTransaction->updatedClassAttributes;
$idStack->pushAttribute( $o->updatedClassAttributes );
rollBackClassAttributes( $idStack, $updatedClassAttributes );
$idStack->popAttribute();
$updatedTranslatedTexts = $updatesInTransaction->updatedTranslatedText;
$idStack->pushAttribute( $o->updatedTranslatedText );
rollBackTranslatedTexts( $idStack, $updatedTranslatedTexts );
$idStack->popAttribute();
$updatedTranslatedTextProperties = $updatesInTransaction->updatedTranslatedTextProperty;
$idStack->pushAttribute( $o->updatedTranslatedTextProperty );
rollBackTranslatedTextProperties( $idStack, $updatedTranslatedTextProperties );
$idStack->popAttribute();
$o->updatedLinks = $updatesInTransaction->updatedLink;
$idStack->pushAttribute( $o->updatedLink );
rollBackLinkAttributes( $idStack, $o->updatedLinks );
$idStack->popAttribute();
$o->updatedTexts = $updatesInTransaction->updatedText;
$idStack->pushAttribute( $o->updatedText );
rollBackTextAttributes( $idStack, $o->updatedTexts );
$idStack->popAttribute();
$updatedSyntranses = $updatesInTransaction->updatedSyntranses;
$idStack->pushAttribute( $o->updatedSyntranses );
rollBackSyntranses( $idStack, $updatedSyntranses );
$idStack->popAttribute();
$updatedAlternativeDefinitionTexts = $updatesInTransaction->updatedAlternativeDefinitionText;
$idStack->pushAttribute( $o->updatedAlternativeDefinitionText );
rollBackAlternativeDefinitionTexts( $idStack, $updatedAlternativeDefinitionTexts );
$idStack->popAttribute();
$updatedAlternativeDefinitions = $updatesInTransaction->updatedAlternativeDefinitions;
$idStack->pushAttribute( $o->updatedAlternativeDefinitions );
rollBackAlternativeDefinitions( $idStack, $updatedAlternativeDefinitions );
$idStack->popAttribute();
$updatedCollectionMemberships = $updatesInTransaction->updatedCollectionMembership;
$idStack->pushAttribute( $o->updatedCollectionMembership );
rollBackCollectionMemberships( $idStack, $updatedCollectionMemberships );
$idStack->popAttribute();
$idStack->popAttribute();
$idStack->popKey();
}
}
$dbr->query( "DROP TABLE `{$dc}_bootstrapped_defined_meanings`;" );
$dbr->query( "CREATE TABLE `{$dc}_bootstrapped_defined_meanings` (
`name` VARCHAR(255) NOT NULL ,
`defined_meaning_id` INT NOT NULL);" );
$userId = getUserId( 'Root' );
if ( $userId == - 1 ) {
echo "root user undefined\n";
die;
}
setUser( $userId );
startNewTransaction( $userId, 0, "Script bootstrap class attribute meanings" );
$languageId = 85;
$collectionId = bootstrapCollection( "Class attribute levels", $languageId, "LEVL" );
$meanings = array();
$meanings[$definedMeaningMeaningName] = bootstrapDefinedMeaning( $definedMeaningMeaningName, $languageId, "The combination of an expression and definition in one language defining a concept." );
$meanings[$definitionMeaningName] = bootstrapDefinedMeaning( $definitionMeaningName, $languageId, "A paraphrase describing a concept." );
$meanings[$synTransMeaningName] = bootstrapDefinedMeaning( $synTransMeaningName, $languageId, "A translation or a synonym that is equal or near equal to the concept defined by the defined meaning." );
$meanings[$relationMeaningName] = bootstrapDefinedMeaning( $relationMeaningName, $languageId, "The association of two defined meanings through a specific relation type." );
$meanings[$annotationMeaningName] = bootstrapDefinedMeaning( $annotationMeaningName, $languageId, "Characteristic information of a concept." );
foreach ( $meanings as $internalName => $meaningId ) {
addDefinedMeaningToCollection( $meaningId, $collectionId, $internalName );
$dbr->query( "INSERT INTO `{$dc}_bootstrapped_defined_meanings` (name, defined_meaning_id) " .
"VALUES (" . $dbr->addQuotes( $internalName ) . ", " . $meaningId . ")" );
function bootStrappedDefinedMeanings( $dc ) {
global
$definedMeaningMeaningName, $definitionMeaningName,
$relationMeaningName, $synTransMeaningName,
$annotationMeaningName, $wgCommandLineMode;
$wgCommandLineMode = true;
$dbr = wfGetDB( DB_MASTER );
$dbr->query( "DROP TABLE IF EXISTS `{$dc}_bootstrapped_defined_meanings`;" );
$dbr->query( "CREATE TABLE `{$dc}_bootstrapped_defined_meanings` (
`name` VARCHAR(255) NOT NULL ,
`defined_meaning_id` INT NOT NULL);" );
$userId = getUserId( 'Root' );
if ( $userId == - 1 ) {
echo "root user undefined\n";
return;
}
setUser( $userId );
setDefaultDC( $dc );
$rdc = wdGetDataSetContext();
startNewTransaction( $userId, 0, "Script bootstrap class attribute meanings", $dc );
$languageId = 85;
$collectionId = bootstrapCollection( "Class attribute levels", $languageId, "LEVL" );
$meanings = array();
$meanings[$definedMeaningMeaningName] = bootstrapDefinedMeaning( $definedMeaningMeaningName, $languageId, "The combination of an expression and definition in one language defining a concept." );
$meanings[$definitionMeaningName] = bootstrapDefinedMeaning( $definitionMeaningName, $languageId, "A paraphrase describing a concept." );
$meanings[$synTransMeaningName] = bootstrapDefinedMeaning( $synTransMeaningName, $languageId, "A translation or a synonym that is equal or near equal to the concept defined by the defined meaning." );
$meanings[$relationMeaningName] = bootstrapDefinedMeaning( $relationMeaningName, $languageId, "The association of two defined meanings through a specific relation type." );
$meanings[$annotationMeaningName] = bootstrapDefinedMeaning( $annotationMeaningName, $languageId, "Characteristic information of a concept." );
foreach ( $meanings as $internalName => $meaningId ) {
addDefinedMeaningToCollection( $meaningId, $collectionId, $internalName );
$dbr->query( "INSERT INTO `{$dc}_bootstrapped_defined_meanings` (name, defined_meaning_id) " .
"VALUES (" . $dbr->addQuotes( $internalName ) . ", " . $meaningId . ")" );
}
$timestamp = wfTimestampNow();
$dbr->query( "INSERT INTO {$dc}_script_log (time, script_name, comment) " .
"VALUES (" . $timestamp . "," . $dbr->addQuotes( '23 - Bootstrap class attribute meanings.php' ) . "," . $dbr->addQuotes( 'create bootstrap class attribute meanings' ) . ")" );
}
public function saveWithinTransaction() {
global
$wgTitle, $wgUser, $wgRequest;
$summary = $wgRequest->getText( 'summary' );
// Insert transaction information into the DB
startNewTransaction( $wgUser->getID(), wfGetIP(), $summary );
// Perform regular save
$this->save( new QueryAtTransactionInformation( $wgRequest->getInt( 'transaction' ), false ) );
// Update page caches
$wgTitle->invalidateCache();
// Add change to RC log
$now = wfTimestampNow();
RecentChange::notifyEdit( $now, $wgTitle, false, $wgUser, $summary, 0, $now, false, '', 0, 0, 0 );
}
function execute( $par ) {
global $wgOut, $wgUser, $wgRequest;
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_title1' ) );
if ( !$wgUser->isAllowed( 'importtsv' ) ) {
$wgOut->addHTML( wfMsg( 'ow_importtsv_not_allowed' ) );
return false;
}
$dbr = wfGetDB( DB_MASTER );
$dc = wdGetDataSetcontext();
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_importing' ) );
setlocale( LC_ALL, 'en_US.UTF-8' );
if ( $wgRequest->getFileName( 'tsvfile' ) ) {
// *****************
// process tsv
// *****************
require_once( 'WikiDataAPI.php' );
require_once( 'Transaction.php' );
$testRun = $wgRequest->getCheck( 'testrun' );
// lets do some tests first. Is this even a tsv file?
// It is _very_ important that the file is utf-8 encoded.
// also, this is a good time to determine the max line length for the
// fgetcsv function.
$file = fopen( $wgRequest->getFileTempname( 'tsvfile' ), 'r' );
$myLine = "";
$maxLineLength = 0;
while ( $myLine = fgets( $file ) ) {
if ( !preg_match( '/./u', $myLine ) ) {
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_import_failed' ) );
$wgOut->addHTML( wfMsg( 'ow_importtsv_not_utf8' ) );
return false;
}
$maxLineLength = max( $maxLineLength, strlen( $myLine ) + 2 );
}
// start from the beginning again. Check if the column names are valid
rewind( $file );
$columns = fgetcsv( $file, $maxLineLength, "\t" );
// somehow testing for $columns[0] fails sometimes. Byte Order Mark?
if ( !$columns || count( $columns ) <= 2 || $columns[1] != "defining expression" ) {
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_import_failed' ) );
$wgOut->addHTML( wfMsg( 'ow_importtsv_not_tsv' ) );
return false;
}
for ( $i = 2; $i < count( $columns ); $i++ ) {
$columnName = $columns[$i];
$baseName = substr( $columnName, 0, strrpos( $columnName, '_' ) );
if ( $baseName == "definition" || $baseName == "translations" ) {
$langCode = substr( $columnName, strrpos( $columnName, '_' ) + 1 );
if ( !getLanguageIdForIso639_3( $langCode ) ) {
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_import_failed' ) );
$wgOut->addHTML( wfMsg( 'ow_impexptsv_unknown_lang', $langCode ) );
return false;
}
}
else { // column name does not start with definition or translations.
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_import_failed' ) );
$wgOut->addHTML( wfMsg( 'ow_importtsv_bad_columns', $columnName ) );
return false;
}
}
//
// All tests passed. lets get started
//
if ( $testRun ) {
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_test_run_title' ) );
}
else {
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_importing' ) );
}
startNewTransaction( $wgUser->getID(), wfGetIP(), "Bulk import via Special:ImportTSV", $dc ); # this string shouldn't be localized because it will be stored in the db
$row = "";
$line = 1; // actually 2, 1 was the header, but increased at the start of while
$definitions = 0; // definitions added
$translations = 0; // translations added
while ( $row = fgetcsv( $file, $maxLineLength, "\t" ) ) {
$line++;
$dmid = $row[0];
$exp = $row[1];
// find the defined meaning record
$qry = "SELECT dm.meaning_text_tcid, exp.spelling ";
$qry .= "FROM {$dc}_defined_meaning dm INNER JOIN {$dc}_expression exp ON dm.expression_id=exp.expression_id ";
$qry .= "WHERE dm.defined_meaning_id=$dmid ";
$qry .= "AND " . getLatestTransactionRestriction( 'dm' );
$qry .= "AND " . getLatestTransactionRestriction( 'exp' );
$dmResult = $dbr->query( $qry );
$dmRecord = null;
// perfomr some tests
if ( $dmRecord = $dbr->fetchRow( $dmResult ) ) {
if ( $dmRecord['spelling'] != $exp ) {
$wgOut->addHTML( "Skipped line $line: defined meaning id $dmid does not match defining expression. Should be '{$dmRecord['spelling']}', found '$exp'.<br />" );
continue;
}
}
else {
$wgOut->addHTML( "Skipped line $line: unknown defined meaning id $dmid. The id may have been altered in the imported file, or the defined meaning or defining expression was removed from the database.<br />" );
continue;
}
// all is well. Get the translated content id
$tcid = $dmRecord['meaning_text_tcid'];
for ( $columnIndex = 2; $columnIndex < count( $columns ); $columnIndex++ ) {
// Google docs removes empty columns at the end of a row,
// so if column index is higher than the length of the row, we can break
// and move on to the next defined meaning.
if ( columnIndex >= count( $row ) ) {
break;
}
$columnValue = $row[$columnIndex];
if ( !$columnValue ) {
continue;
}
$columnName = $columns[$columnIndex];
$langCode = substr( $columnName, strrpos( $columnName, '_' ) + 1 );
$langId = getLanguageIdForIso639_3( $langCode );
if ( strpos( $columnName, 'definition' ) === 0 ) {
if ( !translatedTextExists( $tcid, $langId ) ) {
if ( $testRun ) {
$wgOut->addHTML( "Would add definition for $exp ($dmid) in $langCode: $columnValue.<br />" );
} else {
addTranslatedText( $tcid, $langId, $columnValue );
$wgOut->addHTML( "Added definition for $exp ($dmid) in $langCode: $columnValue.<br />" );
$definitions++;
}
}
}
if ( strpos( $columnName, 'translation' ) === 0 ) {
$spellings = explode( '|', $columnValue );
foreach ( $spellings as $spelling ) {
$spelling = trim( $spelling );
$expression = findExpression( $spelling, $langId );
if ( !$expression ) { // expression does not exist
if ( $testRun ) {
$wgOut->addHTML( "Would add translation for $exp ($dmid) in $langCode: $spelling. Would also add new page.<br />" );
}
else {
$expression = createExpression( $spelling, $langId );
$expression->bindToDefinedMeaning( $dmid, 1 );
// not nescesary to check page exists, createPage does that.
$title = getPageTitle( $spelling );
createPage( 16, $title );
$wgOut->addHTML( "Added translation for $exp ($dmid) in $langCode: $spelling. Also added new page.<br />" );
$translations++;
}
}
else { // expression exists, but may not be bound to this defined meaning.
if ( !$expression->isBoundToDefinedMeaning( $dmid ) ) {
if ( $testRun ) {
$wgOut->addHTML( "Would add translation for $exp ($dmid) in $langCode: $spelling.<br />" );
}
else {
$expression->bindToDefinedMeaning( $dmid, 1 );
$wgOut->addHTML( "Added translation for $exp ($dmid) in $langCode: $spelling.<br />" );
$translations++;
}
}
}
}
}
}
}
if ( $definitions == 0 && $translations == 0 ) {
$wgOut->addHTML( "<br />" );
if ( $testRun ) {
$wgOut->addHTML( wfMsg( 'ow_importtsv_nothing_added_test' ) );
}
else {
$wgOut->addHTML( wfMsg( 'ow_importtsv_nothing_added' ) );
}
$wgOut->addHTML( "<br />" );
}
else {
$wgOut->addHTML( "<br />" . wfMsgExt( 'ow_importtsv_results', 'parsemag', $definitions, $translations ) . "<br />" );
}
}
else {
// render the page
$wgOut->setPageTitle( wfMsg( 'ow_importtsv_title2' ) );
$wgOut->addHTML( wfMsg( 'ow_importtsv_header' ) );
$wgOut->addHTML( getOptionPanelForFileUpload(
array(
wfMsg( 'ow_importtsv_file' ) => getFileField( 'tsvfile' ),
wfMsg( 'ow_importtsv_test_run' ) => getCheckBox( 'testrun', true )
)
) );
}
}
/**
* FIXME - work in progress
*/
public function saveWithinTransaction() {
# global
# $wgTitle, $wgUser, $wgRequest;
global
$wgUser, $wgOut;
if ( !$wgUser->isAllowed( 'wikidata-copy' ) ) {
$wgOut->addWikiText( wfMsgSc( "noedit", $dc->fetchName() ) );
$wgOut->setPageTitle( wfMsgSc( "noedit_title" ) );
return false;
}
# $summary = $wgRequest->getText('summary');
// Insert transaction information into the DB
# startNewTransaction($wgUser->getID(), wfGetIP(), $summary);
startNewTransaction( 0, "0.0.0.0", "copy operation" );
// Perform regular save
# $this->save(new QueryAtTransactionInformation($wgRequest->getInt('transaction'), false));
$newDefinedMeaningId = $this->save();
// Update page caches
# Title::touchArray(array($wgTitle));
// Add change to RC log
# $now = wfTimestampNow();
# RecentChange::notifyEdit($now, $wgTitle, false, $wgUser, $summary, 0, $now, false, '', 0, 0, 0);
return $newDefinedMeaningId;
}
$beginTime = time();
$wgCommandLineMode = true;
$wdDefaultViewDataSet = 'umls';
$arg = reset( $argv );
if ( $arg !== false ) {
$wdDefaultViewDataSet = next( $argv );
}
/*
* User IDs to use during the import of both UMLS and Swiss-Prot
*/
$nlmUserID = getUserId( $wdDefaultViewDataSet );
if ( $nlmUserId == - 1 ) {
echo "Swiss-Prot user not defined in the database.\n";
die;
}
$wgUser->setID( $nlmUserID );
startNewTransaction( $nlmUserID, 0, "UMLS Import" );
echo "Importing UMLS\n";
$umlsImport = importUMLSFromDatabase( "localhost", "umls2007aa", "root", "crosby9" );// , array("NCI", "GO"));
// $umlsImport = importUMLSFromDatabase("localhost", "umls", "root", "nicheGod", array("GO", "SRC", "NCI", "HUGO"));
// $umlsImport = importUMLSFromDatabase("localhost", "umls", "root", NULL, array("GO", "SRC", "NCI", "HUGO"));
$endTime = time();
echo "\n\nTime elapsed: " . durationToString( $endTime - $beginTime );
?>
// $nlmUserID = $sibUserID;
// $wgUser->setID($nlmUserID);
// startNewTransaction($nlmUserID, 0, "UMLS Import");
// echo "Importing UMLS\n";
// $umlsImport = importUMLSFromDatabase("localhost", "umls", "root", "", array("NCI", "GO"));
// $umlsImport = importUMLSFromDatabase("localhost", "umls", "root", "nicheGod", array("GO", "SRC", "NCI", "HUGO"));
// $umlsImport = importUMLSFromDatabase("localhost", "umls", "root", NULL, array("GO", "SRC", "NCI", "HUGO"));
// $EC2GoMapping = loadEC2GoMapping($linkEC2GoFileName);
// $SP2GoMapping = loadSwissProtKeyWord2GoMapping($linkSwissProtKeyWord2GoFileName);
ini_set( 'memory_limit', '256M' );
$wgUser->setID( $sibUserID );
startNewTransaction( $sibUserID, 0, "Swiss-Prot Import" );
echo "\nImporting Swiss-Prot\n";
# $nsstore=wfGetNamespaceStore();
# print_r($nsstore->nsarray);
# "Namespace id for expression=" . MWNamespace::getIndexForName('expression');
// $umlsImport = new UMLSImportResult;
// $umlsImport->umlsCollectionId = 5;
// $umlsImport->sourceAbbreviations['GO'] = 30;
// $umlsImport->sourceAbbreviations['HUGO'] = 69912;
// importSwissProt($swissProtXMLFileName, $umlsImport->umlsCollectionId, $umlsImport->sourceAbbreviations['GO'], $umlsImport->sourceAbbreviations['HUGO'], $EC2GoMapping, $SP2GoMapping);
importSwissProt( $swissProtXMLFileName );
$endTime = time();
echo "\n\nTime elapsed: " . durationToString( $endTime - $beginTime );
