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Merge pull request #2946 from nsoranzo/binascii_reduction

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Remove unnecessary use of binascii
This commit is contained in:
Martin Cech
2016-09-21 12:47:10 -04:00
committed by GitHub
parent b30d331a81 36b514c6e9
commit c81ec07c6d
4 changed files with 41 additions and 43 deletions
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.ci/flake8_lint_include_list.txt
+2
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@@ -13,6 +13,7 @@ lib/galaxy/dataset_collections/structure.py
lib/galaxy/dataset_collections/subcollections.py
lib/galaxy/dataset_collections/type_description.py
lib/galaxy/datatypes/assembly.py
lib/galaxy/datatypes/binary.py
lib/galaxy/datatypes/constructive_solid_geometry.py
lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
@@ -39,6 +40,7 @@ lib/galaxy/datatypes/converters/maf_to_interval_converter.py
lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
lib/galaxy/datatypes/coverage.py
lib/galaxy/datatypes/binary.py
+35 -36
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@@ -12,12 +12,11 @@ import tempfile
import zipfile
import pysam
from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE
from galaxy.datatypes.metadata import MetadataElement, MetadataParameter, ListParameter, DictParameter
from galaxy.datatypes import metadata
from galaxy.util import nice_size, sqlite, which, FILENAME_VALID_CHARS
from galaxy.datatypes.metadata import DictParameter, ListParameter, MetadataElement, MetadataParameter
from galaxy.util import FILENAME_VALID_CHARS, nice_size, sqlite, which
from . import data, dataproviders
@@ -115,8 +114,8 @@ class Idat( Binary ):
def sniff( self, filename ):
try:
header = open( filename ).read(4)
if binascii.b2a_hex( header ) == binascii.hexlify( 'IDAT' ):
header = open( filename, 'rb' ).read(4)
if header == b'IDAT':
return True
return False
except:
@@ -398,7 +397,7 @@ class Bam( Binary ):
# The first 4 bytes of any bam file is 'BAM\1', and the file is binary.
try:
header = gzip.open( filename ).read(4)
if binascii.b2a_hex( header ) == binascii.hexlify( 'BAM\1' ):
if header == b'BAM\1':
return True
return False
except:
@@ -523,9 +522,9 @@ class CRAM( Binary ):
def get_cram_version( self, filename):
try:
with open( filename, "r") as fh:
with open( filename, "rb") as fh:
header = fh.read(6)
return ord( header[4] ), ord( header[5] )
return ord( header[4] ), ord( header[5] )
except Exception as exc:
log.warning( '%s, get_cram_version Exception: %s', self, exc )
return -1, -1
@@ -564,8 +563,8 @@ class CRAM( Binary ):
def sniff( self, filename ):
try:
header = open( filename ).read(4)
if header[0:4] == "CRAM":
header = open( filename, 'rb' ).read(4)
if header == b"CRAM":
return True
return False
except:
@@ -587,7 +586,7 @@ class Bcf( Binary):
# The first 3 bytes of any bcf file is 'BCF', and the file is binary.
try:
header = gzip.open( filename ).read(3)
if binascii.b2a_hex( header ) == binascii.hexlify( 'BCF' ):
if header == b'BCF':
return True
return False
except:
@@ -646,7 +645,7 @@ class H5( Binary ):
def sniff( self, filename ):
# The first 8 bytes of any hdf5 file are 0x894844460d0a1a0a
try:
header = open( filename ).read(8)
header = open( filename, 'rb' ).read(8)
if header == self._magic:
return True
return False
@@ -703,8 +702,8 @@ class Sff( Binary ):
# The first 4 bytes of any sff file is '.sff', and the file is binary. For details
# about the format, see http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format
try:
header = open( filename ).read(4)
if binascii.b2a_hex( header ) == binascii.hexlify( '.sff' ):
header = open( filename, 'rb' ).read(4)
if header == b'.sff':
return True
return False
except:
@@ -748,7 +747,7 @@ class BigWig(Binary):
def sniff( self, filename ):
try:
magic = self._unpack( "I", open( filename ) )
magic = self._unpack( "I", open( filename, 'rb' ) )
return magic[0] == self._magic
except:
return False
@@ -795,8 +794,8 @@ class TwoBit (Binary):
# All twobit files start with a 16-byte header. If the file is smaller than 16 bytes, it's obviously not a valid twobit file.
if os.path.getsize(filename) < 16:
return False
input = open(filename)
magic = struct.unpack(">L", input.read(TWOBIT_MAGIC_SIZE))[0]
header = open(filename, 'rb').read(TWOBIT_MAGIC_SIZE)
magic = struct.unpack(">L", header)[0]
if magic == TWOBIT_MAGIC_NUMBER or magic == TWOBIT_MAGIC_NUMBER_SWAP:
return True
except IOError:
@@ -864,8 +863,8 @@ class SQlite ( Binary ):
# The first 16 bytes of any SQLite3 database file is 'SQLite format 3\0', and the file is binary. For details
# about the format, see http://www.sqlite.org/fileformat.html
try:
header = open(filename).read(16)
if binascii.b2a_hex(header) == binascii.hexlify('SQLite format 3\0'):
header = open(filename, 'rb').read(16)
if header == b'SQLite format 3\0':
return True
return False
except:
@@ -1074,8 +1073,8 @@ class Sra( Binary ):
For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure
"""
try:
header = open(filename).read(8)
if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
header = open(filename, 'rb').read(8)
if header == b'NCBI.sra':
return True
else:
return False
@@ -1104,14 +1103,14 @@ class RData( Binary ):
file_ext = 'RData'
def sniff( self, filename ):
rdata_header = binascii.hexlify('RDX2\nX\n')
rdata_header = b'RDX2\nX\n'
try:
header = open(filename).read(7)
if binascii.b2a_hex(header) == rdata_header:
header = open(filename, 'rb').read(7)
if header == rdata_header:
return True
header = gzip.open( filename ).read(7)
if binascii.b2a_hex(header) == rdata_header:
if header == rdata_header:
return True
except:
return False
@@ -1124,12 +1123,12 @@ class OxliBinary(Binary):
@staticmethod
def _sniff(filename, oxlitype):
try:
with open(filename) as fileobj:
with open(filename, 'rb') as fileobj:
header = fileobj.read(4)
if binascii.b2a_hex(header) == binascii.hexlify('OXLI'):
if header == b'OXLI':
fileobj.read(1) # skip the version number
ftype = fileobj.read(1)
if binascii.b2a_hex(ftype) == oxlitype:
if binascii.hexlify(ftype) == oxlitype:
return True
return False
except IOError:
@@ -1154,7 +1153,7 @@ class OxliCountGraph(OxliBinary):
"""
def sniff(self, filename):
return OxliBinary._sniff(filename, "01")
return OxliBinary._sniff(filename, b"01")
Binary.register_sniffable_binary_format("oxli.countgraph", "oxlicg",
OxliCountGraph)
@@ -1178,7 +1177,7 @@ class OxliNodeGraph(OxliBinary):
"""
def sniff(self, filename):
return OxliBinary._sniff(filename, "02")
return OxliBinary._sniff(filename, b"02")
Binary.register_sniffable_binary_format("oxli.nodegraph", "oxling",
OxliNodeGraph)
@@ -1203,7 +1202,7 @@ class OxliTagSet(OxliBinary):
"""
def sniff(self, filename):
return OxliBinary._sniff(filename, "03")
return OxliBinary._sniff(filename, b"03")
Binary.register_sniffable_binary_format("oxli.tagset", "oxlits", OxliTagSet)
@@ -1224,7 +1223,7 @@ class OxliStopTags(OxliBinary):
"""
def sniff(self, filename):
return OxliBinary._sniff(filename, "04")
return OxliBinary._sniff(filename, b"04")
Binary.register_sniffable_binary_format("oxli.stoptags", "oxlist",
OxliStopTags)
@@ -1249,7 +1248,7 @@ class OxliSubset(OxliBinary):
"""
def sniff(self, filename):
return OxliBinary._sniff(filename, "05")
return OxliBinary._sniff(filename, b"05")
Binary.register_sniffable_binary_format("oxli.subset", "oxliss", OxliSubset)
@@ -1273,7 +1272,7 @@ class OxliGraphLabels(OxliBinary):
"""
def sniff(self, filename):
return OxliBinary._sniff(filename, "06")
return OxliBinary._sniff(filename, b"06")
Binary.register_sniffable_binary_format("oxli.graphlabels", "oxligl",
OxliGraphLabels)
@@ -1354,9 +1353,9 @@ class NetCDF( Binary ):
def sniff( self, filename ):
try:
with open( filename, 'r' ) as f:
with open( filename, 'rb' ) as f:
header = f.read(3)
if binascii.b2a_hex( header ) == binascii.hexlify( 'CDF' ):
if header == b'CDF':
return True
return False
except:
lib/galaxy/datatypes/proteomics.py
+3 -5
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@@ -1,7 +1,6 @@
"""
Proteomics Datatypes
"""
import binascii
import logging
import re
@@ -272,10 +271,9 @@ class ThermoRAW(Binary):
# This combination represents 17 bytes, but to play safe we read 20 bytes from
# the start of the file.
try:
header = open(filename).read(20)
hexheader = binascii.b2a_hex(header)
finnigan = binascii.hexlify('F\0i\0n\0n\0i\0g\0a\0n')
if hexheader.find(finnigan) != -1:
header = open(filename, 'rb').read(20)
finnigan = b'F\0i\0n\0n\0i\0g\0a\0n'
if header.find(finnigan) != -1:
return True
return False
except:
lib/galaxy/util/checkers.py
+1 -2
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@@ -1,4 +1,3 @@
import binascii
import bz2
import gzip
import imghdr
@@ -95,7 +94,7 @@ def check_gzip( file_path ):
# for sff format.
try:
header = gzip.open( file_path ).read(4)
if binascii.b2a_hex( header ) == binascii.hexlify( '.sff' ):
if header == b'.sff':
return ( True, True )
except:
return( False, False )