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Source code for galaxy.datatypes.sniff

"""
File format detector
"""
from __future__ import absolute_import

import gzip
import bz2
import logging
import os
import re
import shutil
import sys
import tempfile
import zipfile

from encodings import search_function as encodings_search_function
from six import text_type

from galaxy import util
from galaxy.util import multi_byte
from galaxy.util import (
    compression_utils,
    unicodify
)
from galaxy.util.checkers import (
    check_binary,
    check_html,
    is_bz2,
    is_gzip
)
from galaxy.datatypes.binary import Binary

log = logging.getLogger(__name__)


[docs]def get_test_fname(fname): """Returns test data filename""" path, name = os.path.split(__file__) full_path = os.path.join(path, 'test', fname) return full_path
[docs]def stream_to_open_named_file( stream, fd, filename, source_encoding=None, source_error='strict', target_encoding=None, target_error='strict' ): """Writes a stream to the provided file descriptor, returns the file's name and bool( is_multi_byte ). Closes file descriptor""" # signature and behavor is somewhat odd, due to backwards compatibility, but this can/should be done better CHUNK_SIZE = 1048576 data_checked = False is_compressed = False is_binary = False is_multi_byte = False if not target_encoding or not encodings_search_function( target_encoding ): target_encoding = util.DEFAULT_ENCODING # utf-8 if not source_encoding: source_encoding = util.DEFAULT_ENCODING # sys.getdefaultencoding() would mimic old behavior (defaults to ascii) while True: chunk = stream.read( CHUNK_SIZE ) if not chunk: break if not data_checked: # See if we're uploading a compressed file if zipfile.is_zipfile( filename ): is_compressed = True else: try: if text_type( chunk[:2] ) == text_type( util.gzip_magic ): is_compressed = True except: pass if not is_compressed: # See if we have a multi-byte character file chars = chunk[:100] is_multi_byte = multi_byte.is_multi_byte( chars ) if not is_multi_byte: is_binary = util.is_binary( chunk ) data_checked = True if not is_compressed and not is_binary: if not isinstance( chunk, text_type ): chunk = chunk.decode( source_encoding, source_error ) os.write( fd, chunk.encode( target_encoding, target_error ) ) else: # Compressed files must be encoded after they are uncompressed in the upload utility, # while binary files should not be encoded at all. os.write( fd, chunk ) os.close( fd ) return filename, is_multi_byte
[docs]def stream_to_file( stream, suffix='', prefix='', dir=None, text=False, **kwd ): """Writes a stream to a temporary file, returns the temporary file's name""" fd, temp_name = tempfile.mkstemp( suffix=suffix, prefix=prefix, dir=dir, text=text ) return stream_to_open_named_file( stream, fd, temp_name, **kwd )
[docs]def check_newlines( fname, bytes_to_read=52428800 ): """ Determines if there are any non-POSIX newlines in the first number_of_bytes (by default, 50MB) of the file. """ CHUNK_SIZE = 2 ** 20 f = open( fname, 'r' ) for chunk in f.read( CHUNK_SIZE ): if f.tell() > bytes_to_read: break if chunk.count( '\r' ): f.close() return True f.close() return False
[docs]def convert_newlines( fname, in_place=True, tmp_dir=None, tmp_prefix=None ): """ Converts in place a file from universal line endings to Posix line endings. >>> fname = get_test_fname('temp.txt') >>> open(fname, 'wt').write("1 2\\r3 4") >>> convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir()) (2, None) >>> open(fname).read() '1 2\\n3 4\\n' """ fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir ) fp = os.fdopen( fd, "wt" ) i = None for i, line in enumerate( open( fname, "U" ) ): fp.write( "%s\n" % line.rstrip( "\r\n" ) ) fp.close() if i is None: i = 0 else: i += 1 if in_place: shutil.move( temp_name, fname ) # Return number of lines in file. return ( i, None ) else: return ( i, temp_name )
[docs]def sep2tabs( fname, in_place=True, patt="\\s+" ): """ Transforms in place a 'sep' separated file to a tab separated one >>> fname = get_test_fname('temp.txt') >>> open(fname, 'wt').write("1 2\\n3 4\\n") >>> sep2tabs(fname) (2, None) >>> open(fname).read() '1\\t2\\n3\\t4\\n' """ regexp = re.compile( patt ) fd, temp_name = tempfile.mkstemp() fp = os.fdopen( fd, "wt" ) i = None for i, line in enumerate( open( fname ) ): line = line.rstrip( '\r\n' ) elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) fp.close() if i is None: i = 0 else: i += 1 if in_place: shutil.move( temp_name, fname ) # Return number of lines in file. return ( i, None ) else: return ( i, temp_name )
[docs]def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix=None ): """ Combines above methods: convert_newlines() and sep2tabs() so that files do not need to be read twice >>> fname = get_test_fname('temp.txt') >>> open(fname, 'wt').write("1 2\\r3 4") >>> convert_newlines_sep2tabs(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir()) (2, None) >>> open(fname).read() '1\\t2\\n3\\t4\\n' """ regexp = re.compile( patt ) fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir ) fp = os.fdopen( fd, "wt" ) for i, line in enumerate( open( fname, "U" ) ): line = line.rstrip( '\r\n' ) elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) fp.close() if in_place: shutil.move( temp_name, fname ) # Return number of lines in file. return ( i + 1, None ) else: return ( i + 1, temp_name )
[docs]def get_headers( fname, sep, count=60, is_multi_byte=False ): """ Returns a list with the first 'count' lines split by 'sep' >>> fname = get_test_fname('complete.bed') >>> get_headers(fname,'\\t') [['chr7', '127475281', '127491632', 'NM_000230', '0', '+', '127486022', '127488767', '0', '3', '29,172,3225,', '0,10713,13126,'], ['chr7', '127486011', '127488900', 'D49487', '0', '+', '127486022', '127488767', '0', '2', '155,490,', '0,2399']] """ headers = [] in_file = compression_utils.get_fileobj(fname) try: for idx, line in enumerate(in_file): line = line.rstrip('\n\r') if is_multi_byte: # TODO: fix this - sep is never found in line line = unicodify( line, 'utf-8' ) sep = sep.encode( 'utf-8' ) headers.append( line.split(sep) ) if idx == count: break finally: in_file.close() return headers
[docs]def is_column_based( fname, sep='\t', skip=0, is_multi_byte=False ): """ Checks whether the file is column based with respect to a separator (defaults to tab separator). >>> fname = get_test_fname('test.gff') >>> is_column_based(fname) True >>> fname = get_test_fname('test_tab.bed') >>> is_column_based(fname) True >>> is_column_based(fname, sep=' ') False >>> fname = get_test_fname('test_space.txt') >>> is_column_based(fname) False >>> is_column_based(fname, sep=' ') True >>> fname = get_test_fname('test_ensembl.tab') >>> is_column_based(fname) True >>> fname = get_test_fname('test_tab1.tabular') >>> is_column_based(fname, sep=' ', skip=0) False >>> fname = get_test_fname('test_tab1.tabular') >>> is_column_based(fname) True """ headers = get_headers( fname, sep, is_multi_byte=is_multi_byte ) count = 0 if not headers: return False for hdr in headers[skip:]: if hdr and hdr[0] and not hdr[0].startswith('#'): if len(hdr) > 1: count = len(hdr) break if count < 2: return False for hdr in headers[skip:]: if hdr and hdr[0] and not hdr[0].startswith('#'): if len(hdr) != count: return False return True
[docs]def guess_ext( fname, sniff_order, is_multi_byte=False ): """ Returns an extension that can be used in the datatype factory to generate a data for the 'fname' file >>> from galaxy.datatypes import registry >>> sample_conf = os.path.join(util.galaxy_directory(), "config", "datatypes_conf.xml.sample") >>> datatypes_registry = registry.Registry() >>> datatypes_registry.load_datatypes(root_dir=util.galaxy_directory(), config=sample_conf) >>> sniff_order = datatypes_registry.sniff_order >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml') >>> guess_ext(fname, sniff_order) 'blastxml' >>> fname = get_test_fname('interval.interval') >>> guess_ext(fname, sniff_order) 'interval' >>> fname = get_test_fname('interval1.bed') >>> guess_ext(fname, sniff_order) 'bed' >>> fname = get_test_fname('test_tab.bed') >>> guess_ext(fname, sniff_order) 'bed' >>> fname = get_test_fname('sequence.maf') >>> guess_ext(fname, sniff_order) 'maf' >>> fname = get_test_fname('sequence.fasta') >>> guess_ext(fname, sniff_order) 'fasta' >>> fname = get_test_fname('file.html') >>> guess_ext(fname, sniff_order) 'html' >>> fname = get_test_fname('test.gtf') >>> guess_ext(fname, sniff_order) 'gtf' >>> fname = get_test_fname('test.gff') >>> guess_ext(fname, sniff_order) 'gff' >>> fname = get_test_fname('gff_version_3.gff') >>> guess_ext(fname, sniff_order) 'gff3' >>> fname = get_test_fname('temp.txt') >>> open(fname, 'wt').write("a\\t2") >>> guess_ext(fname, sniff_order) 'txt' >>> fname = get_test_fname('temp.txt') >>> open(fname, 'wt').write("a\\t2\\nc\\t1\\nd\\t0") >>> guess_ext(fname, sniff_order) 'tabular' >>> fname = get_test_fname('temp.txt') >>> open(fname, 'wt').write("a 1 2 x\\nb 3 4 y\\nc 5 6 z") >>> guess_ext(fname, sniff_order) 'txt' >>> fname = get_test_fname('test_tab1.tabular') >>> guess_ext(fname, sniff_order) 'tabular' >>> fname = get_test_fname('alignment.lav') >>> guess_ext(fname, sniff_order) 'lav' >>> fname = get_test_fname('1.sff') >>> guess_ext(fname, sniff_order) 'sff' >>> fname = get_test_fname('1.bam') >>> guess_ext(fname, sniff_order) 'bam' >>> fname = get_test_fname('3unsorted.bam') >>> guess_ext(fname, sniff_order) 'bam' >>> fname = get_test_fname('test.idpDB') >>> guess_ext(fname, sniff_order) 'idpdb' >>> fname = get_test_fname('test.mz5') >>> guess_ext(fname, sniff_order) 'h5' >>> fname = get_test_fname('issue1818.tabular') >>> guess_ext(fname, sniff_order) 'tabular' >>> fname = get_test_fname('drugbank_drugs.cml') >>> guess_ext(fname, sniff_order) 'cml' >>> fname = get_test_fname('q.fps') >>> guess_ext(fname, sniff_order) 'fps' >>> fname = get_test_fname('drugbank_drugs.inchi') >>> guess_ext(fname, sniff_order) 'inchi' >>> fname = get_test_fname('drugbank_drugs.mol2') >>> guess_ext(fname, sniff_order) 'mol2' >>> fname = get_test_fname('drugbank_drugs.sdf') >>> guess_ext(fname, sniff_order) 'sdf' >>> fname = get_test_fname('5e5z.pdb') >>> guess_ext(fname, sniff_order) 'pdb' >>> fname = get_test_fname('mothur_datatypetest_true.mothur.otu') >>> guess_ext(fname, sniff_order) 'mothur.otu' >>> fname = get_test_fname('1.gg') >>> guess_ext(fname, sniff_order) 'gg' >>> fname = get_test_fname('diamond_db.dmnd') >>> guess_ext(fname, sniff_order) 'dmnd' """ file_ext = None for datatype in sniff_order: """ Some classes may not have a sniff function, which is ok. In fact, the Tabular and Text classes are 2 examples of classes that should never have a sniff function. Since these classes are default classes, they contain few rules to filter out data of other formats, so they should be called from this function after all other datatypes in sniff_order have not been successfully discovered. """ try: if datatype.sniff( fname ): file_ext = datatype.file_ext break except: pass # Ugly hack for tsv vs tabular sniffing, we want to prefer tabular # to tsv but it doesn't have a sniffer - is TSV was sniffed just check # if it is an okay tabular and use that instead. if file_ext == 'tsv': if is_column_based( fname, '\t', 1, is_multi_byte=is_multi_byte ): file_ext = 'tabular' if file_ext is not None: return file_ext headers = get_headers( fname, None ) is_binary = False if is_multi_byte: is_binary = False else: for hdr in headers: for char in hdr: # old behavior had 'char' possibly having length > 1, # need to determine when/if this occurs is_binary = util.is_binary( char ) if is_binary: break if is_binary: break if is_binary: return 'data' # default binary data type file extension if is_column_based( fname, '\t', 1, is_multi_byte=is_multi_byte ): return 'tabular' # default tabular data type file extension return 'txt' # default text data type file extension
[docs]def handle_compressed_file( filename, datatypes_registry, ext='auto' ): CHUNK_SIZE = 2 ** 20 # 1Mb is_compressed = False compressed_type = None keep_compressed = False is_valid = False for compressed_type, check_compressed_function in COMPRESSION_CHECK_FUNCTIONS: is_compressed = check_compressed_function( filename ) if is_compressed: break # found compression type if is_compressed: if ext in AUTO_DETECT_EXTENSIONS: check_exts = COMPRESSION_DATATYPES[ compressed_type ] elif ext in COMPRESSED_EXTENSIONS: check_exts = [ ext ] else: check_exts = [] for compressed_ext in check_exts: compressed_datatype = datatypes_registry.get_datatype_by_extension( compressed_ext ) if compressed_datatype.sniff( filename ): ext = compressed_ext keep_compressed = True is_valid = True break if not is_compressed: is_valid = True elif not keep_compressed: is_valid = True fd, uncompressed = tempfile.mkstemp() compressed_file = DECOMPRESSION_FUNCTIONS[ compressed_type ]( filename ) while True: try: chunk = compressed_file.read( CHUNK_SIZE ) except IOError as e: os.close( fd ) os.remove( uncompressed ) compressed_file.close() raise IOError( 'Problem uncompressing %s data, please try retrieving the data uncompressed: %s' % ( compressed_type, e )) if not chunk: break os.write( fd, chunk ) os.close( fd ) compressed_file.close() # Replace the compressed file with the uncompressed file shutil.move( uncompressed, filename ) return is_valid, ext
[docs]def handle_uploaded_dataset_file( filename, datatypes_registry, ext='auto', is_multi_byte=False ): is_valid, ext = handle_compressed_file( filename, datatypes_registry, ext=ext ) if not is_valid: raise InappropriateDatasetContentError( 'The compressed uploaded file contains inappropriate content.' ) if ext in AUTO_DETECT_EXTENSIONS: ext = guess_ext( filename, sniff_order=datatypes_registry.sniff_order, is_multi_byte=is_multi_byte ) if check_binary( filename ): if not Binary.is_ext_unsniffable(ext) and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ): raise InappropriateDatasetContentError( 'The binary uploaded file contains inappropriate content.' ) elif check_html( filename ): raise InappropriateDatasetContentError( 'The uploaded file contains inappropriate HTML content.' ) return ext
AUTO_DETECT_EXTENSIONS = [ 'auto' ] # should 'data' also cause auto detect? DECOMPRESSION_FUNCTIONS = dict( gzip=gzip.GzipFile, bz2=bz2.BZ2File ) COMPRESSION_CHECK_FUNCTIONS = [ ( 'gzip', is_gzip ), ('bz2', is_bz2) ] COMPRESSION_DATATYPES = dict( gzip=[ 'bam', 'fastq.gz', 'fastqsanger.gz', 'fastqillumina.gz', 'fastqsolexa.gz', 'fastqcssanger.gz'], bz2=['fastq.bz2', 'fastqsanger.bz2', 'fastqillumina.bz2', 'fastqsolexa.bz2', 'fastqcssanger.bz2' ] ) COMPRESSED_EXTENSIONS = [] for exts in COMPRESSION_DATATYPES.values(): COMPRESSED_EXTENSIONS.extend( exts )
[docs]class InappropriateDatasetContentError( Exception ): pass
if __name__ == '__main__': import doctest doctest.testmod(sys.modules[__name__])