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' );
}
}
}
?>
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' ) . ")" );
}
`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 . ")" );
}
$dbr->query( "INSERT INTO {$dc}_script_log (time, script_name, comment) " .
public function __construct( $collectionId, $collectionName, $languageId, $collectionType = "" ) {
$this->collectionId = $collectionId;
$this->languageId = $languageId;
if ( $this->collectionId == 0 )
$this->collectionId = bootstrapCollection( $collectionName, $languageId, $collectionType );
$this->contents = getCollectionContents( $this->collectionId );
}
function importUMLSFromDatabase( $server, $databaseName, $userName, $password, $sources = null ) {
$result = new UMLSImportResult;
openDatabase( $server, $databaseName, $userName, $password );
$languageId = 85;
echo "Creating UMLS collections\n";
$umlsCollectionId = bootstrapCollection( "UMLS", $languageId, "" );
$result->umlsCollectionId = $umlsCollectionId;
$relationCollectionId = bootstrapCollection( "UMLS Relation Types 2005", $languageId, "RELT" );
addDefinedMeaningToCollection( getCollectionMeaningId( $relationCollectionId ), $umlsCollectionId, "rel" );
$relationAttributesCollectionId = bootstrapCollection( "UMLS Relation Attributes 2005", $languageId, "RELT" );
addDefinedMeaningToCollection( $relationAttributesCollectionId, $umlsCollectionId, "rela" );
$semanticNetworkSemanticTypesCollectionId = bootstrapCollection( "Semantic Network 2005AC Semantic Types", $languageId, "CLAS" );
addDefinedMeaningToCollection( getCollectionMeaningId( $semanticNetworkSemanticTypesCollectionId ), $umlsCollectionId, "STY" );
$semanticNetworkRelationTypesCollectionId = bootstrapCollection( "Semantic Network 2005AC Relation Types", $languageId, "RELT" );
addDefinedMeaningToCollection( getCollectionMeaningId( $semanticNetworkRelationTypesCollectionId ), $umlsCollectionId, "RL" );
echo "Loading source abbreviations\n";
$sourceAbbreviations = loadSourceAbbreviations( $sources );
echo "Loading languages\n";
$isoLanguages = loadIsoLanguages();
echo "Importing UMLS terms per source\n";
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
$collectionId = bootstrapCollection( $source, $languageId, "" );
$result->sourceAbbreviations[$sab] = $collectionId;
echo " $i: $sab - $source\n";
importUMLSTerms( $sab, $umlsCollectionId, $collectionId, $languageId, $isoLanguages );
$i++;
}
echo "Importing UMLS definitions per source\n";
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
echo " $i: $sab - $source\n";
importUMLSDefinitions( $sab, $umlsCollectionId, $result->sourceAbbreviations[$sab], $languageId );
$i++;
}
echo "Importing UMLS relation types\n";
importUMLSRelationTypes( $relationCollectionId, $languageId );
echo "Importing UMLS attribute types\n";
importUMLSRelationAttributes( $relationAttributesCollectionId, $languageId );
echo "Importing UMLS relations per source\n";
$relationCollection = getCollectionContents( $relationCollectionId );
$relationAttributesCollection = getCollectionContents( $relationAttributesCollectionId );
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
echo " $i: $sab - $source\n";
$query = "select cui1, cui2, rel from MRREL where sab like '$sab'";
importUMLSRelations( $umlsCollectionId , $relationCollection, $query );
$query = "select cui1, cui2, rela from MRREL where sab like '$sab' and rela!=''";
importUMLSRelations( $umlsCollectionId , $relationAttributesCollection, $query );
$i++;
}
echo "Importing semantic network types\n";
importSNTypes( $semanticNetworkSemanticTypesCollectionId, "SELECT semtypeab,type,definition FROM srdef WHERE type='STY'", $languageId );
importSNTypes( $semanticNetworkRelationTypesCollectionId, "SELECT semtypeab,type,definition FROM srdef WHERE type='RL'", $languageId );
echo "Importing semantic network relations\n";
importSemanticTypeRelations( $semanticNetworkSemanticTypesCollectionId, $relationCollection, "SELECT SEMTYPE1, RELATION, SEMTYPE2 from semtypehier" );
importSemanticTypeRelations( $semanticNetworkRelationTypesCollectionId, $relationCollection, "SELECT RELTYPE1, RELATION, RELTYPE2 from semrelhier" );
echo "Importing UMLS semantic type relations per source\n";
$attributeTypes = getCollectionContents( $semanticNetworkSemanticTypesCollectionId );
$i = 1;
foreach ( $sourceAbbreviations as $sab => $source ) {
echo " " . $i++ . ": $sab - $source\n";
importUMLSSemanticTypes( $sab, $umlsCollectionId, $attributeTypes );
}
return $result;
}
