Source code for galaxy.util.checkers

import gzip
import io
import re
import sys
import tarfile
import zipfile

from six import (
    BytesIO,
    StringIO
)
from six.moves import filter

from galaxy import util
from galaxy.util.image_util import image_type

if sys.version_info < (3, 3):
    gzip.GzipFile.read1 = gzip.GzipFile.read  # workaround for https://bugs.python.org/issue12591
    try:
        import bz2file as bz2
    except ImportError:
        # If bz2file is unavailable, just fallback to not having pbzip2 support.
        import bz2
else:
    import bz2

HTML_CHECK_LINES = 100
CHUNK_SIZE = 2 ** 15  # 32Kb
HTML_REGEXPS = (
    re.compile(r"<A\s+[^>]*HREF[^>]+>", re.I),
    re.compile(r"<IFRAME[^>]*>", re.I),
    re.compile(r"<FRAMESET[^>]*>", re.I),
    re.compile(r"<META[\W][^>]*>", re.I),
    re.compile(r"<SCRIPT[^>]*>", re.I),
)


[docs]def check_html(name, file_path=True): """ Returns True if the file/string contains HTML code. """ # Handles files if file_path is True or text if file_path is False if file_path: temp = io.open(name, "r", encoding='utf-8') else: temp = StringIO(util.unicodify(name)) try: for _ in range(HTML_CHECK_LINES): line = temp.readline(CHUNK_SIZE) if not line: break if any(regexp.search(line) for regexp in HTML_REGEXPS): return True except UnicodeDecodeError: return False finally: temp.close() return False
[docs]def check_binary(name, file_path=True): # Handles files if file_path is True or text if file_path is False if file_path: temp = open(name, "rb") else: temp = BytesIO(name) try: return util.is_binary(temp.read(1024)) finally: temp.close()
[docs]def check_gzip(file_path, check_content=True): # This method returns a tuple of booleans representing ( is_gzipped, is_valid ) # Make sure we have a gzipped file try: with open(file_path, "rb") as temp: magic_check = temp.read(2) if magic_check != util.gzip_magic: return (False, False) except Exception: return (False, False) # We support some binary data types, so check if the compressed binary file is valid # If the file is Bam, it should already have been detected as such, so we'll just check # for sff format. try: with gzip.open(file_path, 'rb') as fh: header = fh.read(4) if header == b'.sff': return (True, True) except Exception: return(False, False) if not check_content: return (True, True) with gzip.open(file_path, mode='rb') as gzipped_file: chunk = gzipped_file.read(CHUNK_SIZE) # See if we have a compressed HTML file if check_html(chunk, file_path=False): return (True, False) return (True, True)
[docs]def check_bz2(file_path, check_content=True): try: with open(file_path, "rb") as temp: magic_check = temp.read(3) if magic_check != util.bz2_magic: return (False, False) except Exception: return(False, False) if not check_content: return (True, True) with bz2.BZ2File(file_path, mode='rb') as bzipped_file: chunk = bzipped_file.read(CHUNK_SIZE) # See if we have a compressed HTML file if check_html(chunk, file_path=False): return (True, False) return (True, True)
[docs]def check_zip(file_path, check_content=True, files=1): if not zipfile.is_zipfile(file_path): return (False, False) if not check_content: return (True, True) chunk = None for filect, member in enumerate(iter_zip(file_path)): handle, name = member chunk = handle.read(CHUNK_SIZE) if chunk and check_html(chunk, file_path=False): return (True, False) if filect >= files: break return (True, True)
[docs]def is_bz2(file_path): is_bz2, is_valid = check_bz2(file_path, check_content=False) return is_bz2
[docs]def is_gzip(file_path): is_gzipped, is_valid = check_gzip(file_path, check_content=False) return is_gzipped
[docs]def is_zip(file_path): is_zipped, is_valid = check_zip(file_path, check_content=False) return is_zipped
def is_single_file_zip(file_path): for i, member in enumerate(iter_zip(file_path)): if i > 1: return False return True def is_tar(file_path): return tarfile.is_tarfile(file_path) def iter_zip(file_path): with zipfile.ZipFile(file_path) as z: for f in filter(lambda x: not x.endswith('/'), z.namelist()): yield (z.open(f), f)
[docs]def check_image(file_path): """ Simple wrapper around image_type to yield a True/False verdict """ if image_type(file_path): return True return False
__all__ = ( 'check_binary', 'check_bz2', 'check_gzip', 'check_html', 'check_image', 'check_zip', 'is_gzip', 'is_bz2', 'is_zip', )