relations.php

<?php

$currentDir = getcwd();

chdir( $currentDir );

if ( php_sapi_name() == 'cli' ) {
	$argsMsg = "Available options :

Note: Parameters are Case sensitive
a)Update => method=update
Params: [type]=[path to score file], Seperate multiple entries by space
Example: php relations.php method=update xref=xref.txt label=label.txt

b)Get Relations => method=relation
Params: [param-name]=[param-value], Separate multiple entries by &
Available Params: pwId_1, pwId_2, minScore, type(xref/label/ontology), species(replace the space with a -)
Example: php relations.php method=relation pwId_1=WP500 pwId_2=WP520 minscore=5 type=xref species=Homo-sapiens\n
";
	if ( $argv[0] == 'relations.php' ) {
		if ( $argc >= 2 ) {
			parse_str( $argv[1], $args );
			switch ( $args['method'] ) {
				case 'update':

					$relationType = [];

					for ( $i = 2; $i < count( $argv ); $i++ ) {
						parse_str( $argv[$i], $params );

						if ( count( $params ) == 0 ) {
							echo "Error: Please enter proper parameters\n\n";
							echo $argsMsg;
						} else {
							foreach ( $params as $type => $file ) {
								if ( $type == '' || $file == '' ) {
									echo "Error in parameters";
									exit();
								}
								$relationType[] = [ 'type' => $type, 'file' => $file ];
							}
						}
					}
					Relations::updateDb( $relationType );
				break;

				case 'relation':

					$type = "";
					$pwId_1 = "";
					$pwId_2 = "";
					$minscore = "";
					$species = "";

					for ( $i = 2; $i < count( $argv ); $i++ ) {
						parse_str( $argv[$i] );
					}

					if ( $species != "" ) {
						$species = str_replace( "-", " ", $species );
					}

// echo $type . " " . $pwId_1 . " " . $pwId_2 . " " . $minscore;

					$results = Relations::fetchRelations( $type, $pwId_1, $pwId_2, $minscore, $species );

					echo "Pathway Id 1\tPathway Id 2\tScore\tRelation type\tSpecies\n";
					if ( count( $results ) > 0 ) {
						foreach ( $results as $relation ) {
							echo "{$relation->pwId_1}\t{$relation->pwId_2}\t{$relation->score}\t{$relation->type}\t{$relation->species}\n";
						}
					}
				break;

				default:
					echo "Error in parameters\n\n";
					echo $argsMsg;
					exit();
			}

		} else {
			echo $argsMsg;
			exit();
		}
	}
}

class Relations {
	public static $_relationsTable = "relations";
	private static $_pathwaySpecies = [];

	public static function lastUpdated() {
		$result['xref'] = date( "F d, Y H:i:s", filemtime( self::$_xrefScoreFile ) );
		$result['label'] = date( "F d, Y H:i:s", filemtime( self::$_labelScoreFile ) );
		return $result;
	}

	public static function checkFile( $file ) {
		if ( !is_file( $file ) ) {
			return false;

  } else { return true;
  }
	}

	private static function refreshTable( $relationType ) {
		$dbw =& wfGetDB( DB_MASTER );
		$sql = "CREATE TABLE IF NOT EXISTS `" . self::$_relationsTable . "` (
					`pwId_1` VARCHAR( 10 ) NOT NULL ,
					`pwId_2` VARCHAR( 10 ) NOT NULL ,
					`type` VARCHAR( 10 ) NOT NULL ,
					`score` FLOAT UNSIGNED NOT NULL,
					`species` VARCHAR( 50 ) NOT NULL
				);";
		$create = $dbw->query( $sql );
		$sql = "Delete FROM "  . self::$_relationsTable . " WHERE type ='" . $relationType . "'";
		$truncate = $dbw->query( $sql );
	}

	public static function updateDb( $relationType ) {
		$dbw =& wfGetDB( DB_MASTER );

		foreach ( $relationType as $method ) {
			if ( !self::checkFile( $method['file'] ) ) {
				echo "Error: File not found! {$method['file']}\n";
				exit();
			}

			// Remove only those type of relations which are being updated.
			self::refreshTable( $method['type'] );

			$file = file( $method['file'] );
			for ( $i = 1; $i < count( $file ); $i++ ) {
				$relation = explode( "\t", trim( $file[$i] ) );

				if ( $relation[2] > 0 ) {
					 $species = self::getSpecies( $relation[0] );
					 $score = self::normalizeScore( $relation[2], $relation[3], $relation[4] );

					 $dbw->insert( self::$_relationsTable, [
													'pwId_1' => $relation[0],
													'pwId_2' => $relation[1],
													'type' => $method['type'],
													'score' => $score,
													'species' => $species
											] );
				}

			}

			unset( $file );
		}
	}

	public static function fetchRelations( $type = '', $pwId_1 = '', $pwId_2 = '', $minScore = 0, $species = '' ) {
		$dbr =& wfGetDB( DB_SLAVE );
		$query = "SELECT * FROM " . self::$_relationsTable;
		$minScore = (float)$minScore;
		$conditions = [];

		if ( $type != '' ) {
			$conditions[] = "type = '$type'";
		}

		if ( $pwId_1 != '' && $pwId_2 != '' ) {
			$conditions[] = "((pwId_1 = '$pwId_1' AND pwId_2 = '$pwId_2') OR (pwId_1 = '$pwId_2' AND pwId_2 = '$pwId_1'))";
		} elseif ( $pwId_1 != '' && $pwId_2 == '' || $pwId_1 == '' && $pwId_2 != '' ) {
			$pwId = ( $pwId_1 == "" ) ? $pwId_2 : $pwId_1;
			$conditions[] = "(pwId_1 = '$pwId' OR pwId_2 = '$pwId')";
		}

		if ( $minScore > 0 ) {
			$conditions[] = "score > $minScore";
		}

		if ( $species != '' ) {
			$conditions[] = "species = '$species'";
		}

		if ( count( $conditions ) > 0 ) {
			$cons = implode( " AND ", $conditions );
			$query .= " Where $cons";
		}

		$res = $dbr->query( $query );
		while ( $row = $dbr->fetchObject( $res ) ) {
			$result[] = $row;
		}
		$dbr->freeResult( $res );

		return $result;
	}

	private static function getSpecies( $pathwayId ) {
		if ( array_key_exists( $pathwayId, self::$_pathwaySpecies ) ) {
			return self::$_pathwaySpecies[$pathwayId];
		} else {
			$pathway = Pathway::newFromTitle( $pathwayId );
			$species = $pathway->getSpecies();
			self::$_pathwaySpecies[$pathwayId] = $species;
			return $species;
		}
	}

	private static function normalizeScore( $score, $pwId_1Count, $pwId_2Count ) {
		return $normalizedScore = $score / min( $pwId_1Count, $pwId_2Count );
	}
}