public function testIteratorNegative()
{
$directoryPath = 'directory/path';
$filePath = $this->filePaths[0];
$this->setExpectedException('UnexpectedValueException', sprintf("Unable to determine a module, file '%s' belongs to.", $filePath));
$this->directoryMock->expects($this->at(0))->method('getAbsolutePath')->with($filePath)->will($this->returnValue($directoryPath . $filePath));
$this->moduleDirResolverMock->expects($this->at(0))->method('getModuleName')->with($directoryPath . $filePath)->will($this->returnValue(false));
$this->directoryMock->expects($this->never())->method('readFile');
$this->fileIterator->current();
}
public function testToArray()
{
$contents = ['content1', 'content2'];
$expectedArray = [];
$index = 0;
foreach ($this->filePaths as $filePath) {
$expectedArray[$filePath] = $contents[$index];
$this->directoryMock->expects($this->at($index))->method('readFile')->with($filePath)->will($this->returnValue($contents[$index++]));
}
$this->assertEquals($expectedArray, $this->fileIterator->toArray());
}
/**
* {@inheritdoc}
*/
public function valid()
{
$current = $this->current();
if ($this->names) {
return count($current) == count($this->names);
}
return parent::valid();
}
$humanBowtieStats = BowtieStatsFinder::getBowtieStatsLogFile($dir->getPathname(), BowtieStatsFinder::HUMAN_FILE);
if (!$humanBowtieStats || !($humanMappingPercent = $humanBowtieStats->getAlignedReadsPercent())) {
$humanMappingPercent = 'NA';
}
$referenceBowtieStats = BowtieStatsFinder::getBowtieStatsLogFile($dir->getPathname(), BowtieStatsFinder::REFERENCE_FILE);
if (!$referenceBowtieStats || !($refernceMappingPercent = $referenceBowtieStats->getAlignedReadsPercent())) {
$relativeToUnmappedMappingPercent = 'NA';
} else {
$relativeToUnmappedMappingPercent = round((100 - $humanMappingPercent) * $refernceMappingPercent / 100, 2);
}
// search for reads filtering stats
$nReadsTotal = 'NA';
$nReadsFiltered = $humanBowtieStats ? $humanBowtieStats->getProcessedReadsCount() : 'NA';
$percentFiltered = 'NA';
$path = $dir->getPathname() . DIRECTORY_SEPARATOR . 'log';
$file = FileIterator::getFileByPattern('/reads-filter\\.pl\\.o\\d+/', $path);
$filepath = $path . DIRECTORY_SEPARATOR . $file;
if ($file == null) {
printf("Warning: file reads-filter.pl.o[:digits:] not found in [%s/log] directory\n", basename($dir->getPathname()));
} else {
if (!file_exists($filepath)) {
printf("Warning: file [%s] not found\n", $filepath);
} else {
$content = file_get_contents($filepath);
$result = preg_match('/Filtered (\\d+) of (\\d+) reads/', $content, $matches);
if ($result == 0) {
printf("Warning: file [%s] has no statistics\n", $filepath);
} else {
$nReadsTotal = $matches[2];
}
}
}
public function fetch()
{
if (!isset($this->fp)) {
$this->fp = fopen($this->filename, "r");
}
if (!feof($this->fp)) {
return $line = fgets($this->fp, 4096);
} else {
fclose($this->fp);
$this->fp = NULL;
return false;
}
}
}
$file = new FileIterator("colors-iterator.php");
while (($line = $file->fetch()) !== false) {
//echo$line."<br/>";
}
class FileIterator2 implements Iterator
{
private $filename;
private $fp = NULL;
public function __construct($file)
{
$this->filename = $file;
}
public function __destruct()
{
fclose($this->fp);
}
/**
* Returns an FileIterator for the files directly in this folder (not recursive).
*
* The returned Iterator will return objects of the type File, but if the second parameter is
* set to FileSystem::RETURN_PATHS just the paths are returned.
*
* The first argument is a regular expression pattern that is used to filter the result. The
* pattern is applied only on the file name, not on the whole path.
* If the first parameter starts with a dot a faster filter only on the file extension will be
* set. This causes that a regular expression pattern can't start with a dot!
*
* @param int Whether to return objects or paths
* @param string Search pattern (regular expression or a file extension starting with a dot)
* @return array Returns the array or null on failrue
*/
public function getFileIterator($pattern = null, $mode = FileSystem::RETURN_OBJECTS) {
$iterator = new FileIterator($this->path);
$iterator->setMode($mode);
if ($pattern !== null) {
if ($pattern !== null && strlen($pattern) > 0 && $pattern[0] == '.') {
$extension = substr($pattern, 1);
$iterator->setExtensionFilter($extension);
}
elseif ($pattern !== null) {
$iterator->setFilter($pattern);
}
}
return $iterator;
}
public function __construct($query, $mysqli_connection)
{
$this->outfile = $mysqli_connection->select_into_outfile($query);
parent::__construct($this->outfile, true);
}
/**
* Define o objeto que será Iterado
* @param File $file
*/
public function setFileObject( File $file ) {
$this->iterator->setFileObject( $file );
}
/**
* @group single
*/
public function testIgnoreNonCompletePaths()
{
$expected = realpath(self::expand('dir2/file.php'));
$iterator = new FileIterator(self::$expectedFiles, [self::expand('dir')]);
$this->assertArrayHasKey($expected, $iterator->toArray(), "'{$expected}' should not be ignored as 'dir' should not match 'dir2'");
}
