Source code for seqenv.common

# Built-in modules #
import tempfile, datetime, dateutil, hashlib

# One liners #
flatter = lambda x: [item for sublist in x for item in sublist]

################################################################################
def new_temp_path(**kwargs):
    """A new temporary path"""
    handle = tempfile.NamedTemporaryFile(**kwargs)
    path = handle.name
    handle.close()
    return path

################################################################################
class GenWithLength(object):
    """A generator with a length attribute"""
    def __init__(self, gen, length): self.gen, self.length = gen, length
    def __iter__(self): return self.gen
    def __len__(self): return self.length

################################################################################
def pretty_now():
    """Returns some thing like '2014-07-24 11:12:45 CEST+0200'"""
    now = datetime.datetime.now(dateutil.tz.tzlocal())
    return now.strftime("%Y-%m-%d %H:%M:%S %Z%z")

################################################################################
def md5sum(file_path, blocksize=65536):
    """Compute the md5 of a file. Pretty fast."""
    md5 = hashlib.md5()
    with open(file_path, "rb") as f:
        for block in iter(lambda: f.read(blocksize), ""):
            md5.update(block)
    return md5.hexdigest()

################################################################################
def download_from_url(source, destination, progress=False, uncompress=True):
    """Download a file from an URL and place it somewhere. Like wget.
    Uses requests and tqdm to display progress if you want.
    By default it will uncompress files."""
    from tqdm import tqdm
    import requests
    response = requests.get(source, stream=True)
    with open(destination, "wb") as handle:
        if progress:
            for data in tqdm(response.iter_content()): handle.write(data)
        else:
            for data in response.iter_content(): handle.write(data)
    if uncompress:
        with open(destination) as f: header = f.read(4)
        if header == "PK\x03\x04": unzip(destination, inplace=True)
        # Add other compression formats here

################################################################################
def unzip(source, destination=None, inplace=False, single=True):
    """Unzip a standard zip file. Can specify the destination of the
    uncompressed file, or just set inplace=True to delete the original."""
    # Load #
    import zipfile, tempfile, shutil
    # Check #
    assert zipfile.is_zipfile(source)
    # Load #
    z = zipfile.ZipFile(source)
    if single or inplace: assert len(z.infolist()) == 1
    # Single file #
    if single:
        member = z.infolist()[0]
        tmpdir = tempfile.mkdtemp() + '/'
        z.extract(member, tmpdir)
        z.close()
        if inplace: shutil.move(tmpdir + member.filename, source)
        else:       shutil.move(tmpdir + member.filename, destination)
    # Multifile - no security, dangerous #
    if not single:
        z.extractall()