import gzip
from mmtf.utils.constants import BASE_URL, BASE_URL_REDUCED
try:
import urllib2
from StringIO import StringIO
except:
import urllib.request as urllib2
from io import BytesIO as StringIO
import msgpack
from .mmtf_reader import MMTFDecoder
from .mmtf_writer import MMTFEncoder,TemplateEncoder
def _internet_on(address):
"""
Check to see if the internet is on by pinging a set address.
:param address: the IP or address to hit
:return: a boolean - true if can be reached, false if not.
"""
try:
urllib2.urlopen(address, timeout=1)
return True
except urllib2.URLError as err:
return False
def write_mmtf(file_path, input_data, input_function):
"""API function to write data as MMTF to a file
:param file_path the path of the file to write
:param input_data the input data in any user format
:param input_function a function to converte input_data to an output format. Must contain all methods in TemplateEncoder
"""
mmtf_encoder = MMTFEncoder()
pass_data_on(input_data, input_function, mmtf_encoder)
mmtf_encoder.write_file(file_path)
def pass_data_on(input_data, input_function, output_data):
"""Helper to pass data from one data structure to another.
:param input_data the input data in any user format
:param input_function a function to converte input_data to an output format. Must contain all methods in TemplateEncoder.
:param output_data a data holder for the data to be put into."""
input_function(input_data, output_data)
return output_data
def get_raw_data_from_url(pdb_id, reduced=False):
"""" Get the msgpack unpacked data given a PDB id.
:param pdb_id: the input PDB id
:return the unpacked data (a dict) """
url = get_url(pdb_id,reduced)
request = urllib2.Request(url)
request.add_header('Accept-encoding', 'gzip')
response = urllib2.urlopen(request)
if response.info().get('Content-Encoding') == 'gzip':
data = ungzip_data(response.read())
else:
data = response.read()
return _unpack(data)
def get_url(pdb_id,reduced=False):
"""Get the URL for the data for a given PDB id.
:param pdb_id: the input PDB id
:return the URL for this PDB id"""
if reduced:
return BASE_URL_REDUCED + pdb_id
else:
return BASE_URL + pdb_id
def _unpack(data):
out_data = msgpack.unpackb(data.read(), raw=False)
return out_data
def fetch(pdb_id):
"""Return a decoded API to the data from a PDB id.
:param pdb_id: the input PDB id
:return an API to decoded data """
decoder = MMTFDecoder()
decoder.decode_data(get_raw_data_from_url(pdb_id))
return decoder
def parse(file_path):
"""Return a decoded API to the data from a file path.
:param file_path: the input file path. Data is not entropy compressed (e.g. gzip)
:return an API to decoded data """
newDecoder = MMTFDecoder()
with open(file_path, "rb") as fh:
newDecoder.decode_data(_unpack(fh))
return newDecoder
def parse_gzip(file_path):
"""Return a decoded API to the data from a file path. File is gzip compressed.
:param file_path: the input file path. Data is gzip compressed.
:return an API to decoded data"""
newDecoder = MMTFDecoder()
newDecoder.decode_data(_unpack(gzip.open(file_path, "rb")))
return newDecoder
def ungzip_data(input_data):
"""Return a string of data after gzip decoding
:param the input gziped data
:return the gzip decoded data"""
buf = StringIO(input_data)
f = gzip.GzipFile(fileobj=buf)
return f
