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Source code for galaxy.datatypes.sniff

File format detector

import bz2
import codecs
import gzip
import io
import logging
import os
import re
import shutil
import sys
import tempfile
import urllib.request
import zipfile

from galaxy import util
from galaxy.util import compression_utils
from galaxy.util.checkers import (

log = logging.getLogger(__name__)

SNIFF_PREFIX_BYTES = int(os.environ.get("GALAXY_SNIFF_PREFIX_BYTES", None) or 2 ** 20)

[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_url_to_file(path, file_sources=None): prefix = "url_paste" if file_sources and file_sources.looks_like_uri(path): file_source_path = file_sources.get_file_source_path(path) _, temp_name = tempfile.mkstemp(prefix=prefix) file_source_path.file_source.realize_to(file_source_path.path, temp_name) return temp_name else: page = urllib.request.urlopen(path) # page will be .close()ed in stream_to_file temp_name = stream_to_file(page, prefix=prefix, source_encoding=util.get_charset_from_http_headers(page.headers)) return temp_name
[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 name. Closes file descriptor""" # signature and behavor is somewhat odd, due to backwards compatibility, but this can/should be done better CHUNK_SIZE = 1048576 try: codecs.lookup(target_encoding) except Exception: target_encoding = util.DEFAULT_ENCODING # utf-8 use_source_encoding = source_encoding is not None while True: chunk = stream.read(CHUNK_SIZE) if not chunk: break if use_source_encoding: # If a source encoding is given we use it to convert to the target encoding try: if not isinstance(chunk, str): chunk = chunk.decode(source_encoding, source_error) os.write(fd, chunk.encode(target_encoding, target_error)) except UnicodeDecodeError: use_source_encoding = False os.write(fd, chunk) else: # Compressed files must be encoded after they are uncompressed in the upload utility, # while binary files should not be encoded at all. if isinstance(chunk, str): chunk = chunk.encode(target_encoding, target_error) os.write(fd, chunk) os.close(fd) return filename
[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 handle_composite_file(datatype, src_path, extra_files, name, is_binary, tmp_dir, tmp_prefix, upload_opts): if not is_binary: if upload_opts.get('space_to_tab'): convert_newlines_sep2tabs(src_path, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix) else: convert_newlines(src_path, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix) file_output_path = os.path.join(extra_files, name) shutil.move(src_path, file_output_path) # groom the dataset file content if required by the corresponding datatype definition if datatype and datatype.dataset_content_needs_grooming(file_output_path): datatype.groom_dataset_content(file_output_path)
[docs]def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload", block_size=128 * 1024, regexp=None): """ Converts in place a file from universal line endings to Posix line endings. """ fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir) i = 0 NEWLINE_BYTE = 10 CR_BYTE = 13 with open(fd, mode="wb") as fp, open(fname, mode="rb") as fi: last_char = None block = fi.read(block_size) last_block = b"" while block: if last_char == CR_BYTE and block.startswith(b"\n"): # Last block ended with CR, new block startswith newline. # Since we replace CR with newline in the previous iteration we skip the first byte block = block[1:] if block: last_char = block[-1] block = block.replace(b"\r\n", b"\n").replace(b"\r", b"\n") if regexp: block = b"\t".join(regexp.split(block)) fp.write(block) i += block.count(b"\n") last_block = block block = fi.read(block_size) if last_block and last_block[-1] != NEWLINE_BYTE: i += 1 fp.write(b"\n") 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=br"[^\S\n]+", tmp_dir=None, tmp_prefix="gxupload"): """ Converts newlines in a file to posix newlines and replaces spaces with tabs. >>> fname = get_test_fname('temp.txt') >>> with open(fname, 'wt') as fh: ... _ = fh.write(u"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) return convert_newlines(fname, in_place, tmp_dir, tmp_prefix, regexp=regexp)
[docs]def iter_headers(fname_or_file_prefix, sep, count=60, comment_designator=None): idx = 0 if isinstance(fname_or_file_prefix, FilePrefix): file_iterator = fname_or_file_prefix.line_iterator() else: file_iterator = compression_utils.get_fileobj(fname_or_file_prefix) for line in file_iterator: line = line.rstrip('\n\r') if comment_designator is not None and comment_designator != '' and line.startswith(comment_designator): continue yield line.split(sep) idx += 1 if idx == count: break
[docs]def validate_tabular(fname_or_file_prefix, validate_row, sep, comment_designator=None): for row in iter_headers(fname_or_file_prefix, sep, count=-1, comment_designator=comment_designator): validate_row(row)
[docs]def get_headers(fname_or_file_prefix, sep, count=60, comment_designator=None): """ Returns a list with the first 'count' lines split by 'sep', ignoring lines starting with 'comment_designator' >>> 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']] True >>> fname = get_test_fname('test.gff') >>> get_headers(fname, '\\t', count=5, comment_designator='#') == [[''], ['chr7', 'bed2gff', 'AR', '26731313', '26731437', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731491', '26731536', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731541', '26731649', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731659', '26731841', '.', '+', '.', 'score']] True """ return list(iter_headers(fname_or_file_prefix=fname_or_file_prefix, sep=sep, count=count, comment_designator=comment_designator))
[docs]def is_column_based(fname_or_file_prefix, sep='\t', skip=0): """ 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.tabular') >>> 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 """ if getattr(fname_or_file_prefix, "binary", None) is True: return False try: headers = get_headers(fname_or_file_prefix, sep) except UnicodeDecodeError: return False 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_binary=False): """ Returns an extension that can be used in the datatype factory to generate a data for the 'fname' file >>> from galaxy.datatypes.registry import example_datatype_registry_for_sample >>> datatypes_registry = example_datatype_registry_for_sample() >>> sniff_order = datatypes_registry.sniff_order >>> fname = get_test_fname('empty.txt') >>> guess_ext(fname, sniff_order) 'txt' >>> 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('interv1.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('1.genbank') >>> guess_ext(fname, sniff_order) 'genbank' >>> fname = get_test_fname('1.genbank.gz') >>> guess_ext(fname, sniff_order) 'genbank.gz' >>> 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.gff3') >>> guess_ext(fname, sniff_order) 'gff3' >>> fname = get_test_fname('2.txt') >>> guess_ext(fname, sniff_order) # 2.txt 'txt' >>> fname = get_test_fname('2.tabular') >>> guess_ext(fname, sniff_order) 'tabular' >>> fname = get_test_fname('3.txt') >>> guess_ext(fname, sniff_order) # 3.txt '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) 'unsorted.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('mothur_datatypetest_true.mothur.lower.dist') >>> guess_ext(fname, sniff_order) 'mothur.lower.dist' >>> fname = get_test_fname('mothur_datatypetest_true.mothur.square.dist') >>> guess_ext(fname, sniff_order) 'mothur.square.dist' >>> fname = get_test_fname('mothur_datatypetest_true.mothur.pair.dist') >>> guess_ext(fname, sniff_order) 'mothur.pair.dist' >>> fname = get_test_fname('mothur_datatypetest_true.mothur.freq') >>> guess_ext(fname, sniff_order) 'mothur.freq' >>> fname = get_test_fname('mothur_datatypetest_true.mothur.quan') >>> guess_ext(fname, sniff_order) 'mothur.quan' >>> fname = get_test_fname('mothur_datatypetest_true.mothur.ref.taxonomy') >>> guess_ext(fname, sniff_order) 'mothur.ref.taxonomy' >>> fname = get_test_fname('mothur_datatypetest_true.mothur.axes') >>> guess_ext(fname, sniff_order) 'mothur.axes' >>> guess_ext(get_test_fname('infernal_model.cm'), sniff_order) 'cm' >>> 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' >>> fname = get_test_fname('1.excel.xls') >>> guess_ext(fname, sniff_order, is_binary=True) 'excel.xls' >>> fname = get_test_fname('biom2_sparse_otu_table_hdf5.biom2') >>> guess_ext(fname, sniff_order) 'biom2' >>> fname = get_test_fname('454Score.pdf') >>> guess_ext(fname, sniff_order) 'pdf' >>> fname = get_test_fname('1.obo') >>> guess_ext(fname, sniff_order) 'obo' >>> fname = get_test_fname('1.arff') >>> guess_ext(fname, sniff_order) 'arff' >>> fname = get_test_fname('1.afg') >>> guess_ext(fname, sniff_order) 'afg' >>> fname = get_test_fname('1.owl') >>> guess_ext(fname, sniff_order) 'owl' >>> fname = get_test_fname('Acanium.snaphmm') >>> guess_ext(fname, sniff_order) 'snaphmm' >>> fname = get_test_fname('wiggle.wig') >>> guess_ext(fname, sniff_order) 'wig' >>> fname = get_test_fname('example.iqtree') >>> guess_ext(fname, sniff_order) 'iqtree' >>> fname = get_test_fname('1.stockholm') >>> guess_ext(fname, sniff_order) 'stockholm' >>> fname = get_test_fname('1.xmfa') >>> guess_ext(fname, sniff_order) 'xmfa' >>> fname = get_test_fname('test.blib') >>> guess_ext(fname, sniff_order) 'blib' >>> fname = get_test_fname('test.phylip') >>> guess_ext(fname, sniff_order) 'phylip' >>> fname = get_test_fname('1.smat') >>> guess_ext(fname, sniff_order) 'smat' >>> fname = get_test_fname('1.ttl') >>> guess_ext(fname, sniff_order) 'ttl' >>> fname = get_test_fname('1.hdt') >>> guess_ext(fname, sniff_order, is_binary=True) 'hdt' >>> fname = get_test_fname('1.phyloxml') >>> guess_ext(fname, sniff_order) 'phyloxml' >>> fname = get_test_fname('1.tiff') >>> guess_ext(fname, sniff_order) 'tiff' >>> fname = get_test_fname('1.fastqsanger.gz') >>> guess_ext(fname, sniff_order) # See test_datatype_registry for more compressed type tests. 'fastqsanger.gz' >>> fname = get_test_fname('1.mtx') >>> guess_ext(fname, sniff_order) 'mtx' >>> fname = get_test_fname('1imzml') >>> guess_ext(fname, sniff_order) # This test case is ensuring doesn't throw exception, actual value could change if non-utf encoding handling improves. 'data' """ file_prefix = FilePrefix(fname) file_ext = run_sniffers_raw(file_prefix, sniff_order, is_binary) # 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(file_prefix, '\t', 1): file_ext = 'tabular' if file_ext is not None: return file_ext # skip header check if data is already known to be binary if is_binary: return file_ext or 'binary' try: get_headers(file_prefix, None) except UnicodeDecodeError: return 'data' # default data type file extension if is_column_based(file_prefix, '\t', 1): return 'tabular' # default tabular data type file extension return 'txt' # default text data type file extension
[docs]def run_sniffers_raw(filename_or_file_prefix, sniff_order, is_binary=False): """Run through sniffers specified by sniff_order, return None of None match. """ if isinstance(filename_or_file_prefix, FilePrefix): fname = filename_or_file_prefix.filename file_prefix = filename_or_file_prefix else: fname = filename_or_file_prefix file_prefix = FilePrefix(filename_or_file_prefix) file_ext = None for datatype in sniff_order: """ Some classes may not have a sniff function, which is ok. In fact, Binary, Data, Tabular and Text are 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 hasattr(datatype, "sniff_prefix"): datatype_compressed = getattr(datatype, "compressed", False) if datatype_compressed and not file_prefix.compressed_format: continue if not datatype_compressed and file_prefix.compressed_format: continue if file_prefix.compressed_format and getattr(datatype, "compressed_format", None): # In this case go a step further and compare the compressed format detected # to the expected. if file_prefix.compressed_format != datatype.compressed_format: continue if datatype.sniff_prefix(file_prefix): file_ext = datatype.file_ext break elif is_binary and not datatype.is_binary: continue elif datatype.sniff(fname): file_ext = datatype.file_ext break except Exception: pass return file_ext
[docs]def zip_single_fileobj(path): z = zipfile.ZipFile(path) for name in z.namelist(): if not name.endswith('/'): return z.open(name)
[docs]class FilePrefix:
[docs] def __init__(self, filename): non_utf8_error = None compressed_format = None contents_header_bytes = None contents_header = None # First MAX_BYTES of the file. truncated = False # A future direction to optimize sniffing even more for sniffers at the top of the list # is to lazy load contents_header based on what interface is requested. For instance instead # of returning a StringIO directly in string_io() return an object that reads the contents and # populates contents_header while providing a StringIO-like interface until the file is read # but then would fallback to native string_io() try: compressed_format, f = compression_utils.get_fileobj_raw(filename, "rb") try: contents_header_bytes = f.read(SNIFF_PREFIX_BYTES) truncated = len(contents_header_bytes) == SNIFF_PREFIX_BYTES contents_header = contents_header_bytes.decode("utf-8") finally: f.close() except UnicodeDecodeError as e: non_utf8_error = e self.truncated = truncated self.filename = filename self.non_utf8_error = non_utf8_error self.binary = non_utf8_error is not None # obviously wrong self.compressed_format = compressed_format self.contents_header = contents_header self.contents_header_bytes = contents_header_bytes self._file_size = None
@property def file_size(self): if self._file_size is None: self._file_size = os.path.getsize(self.filename) return self._file_size
[docs] def string_io(self): if self.non_utf8_error is not None: raise self.non_utf8_error rval = io.StringIO(self.contents_header) return rval
[docs] def startswith(self, prefix): return self.string_io().read(len(prefix)) == prefix
[docs] def line_iterator(self): s = self.string_io() s_len = len(s.getvalue()) for line in s: if line.endswith("\n") or line.endswith("\r"): yield line elif s.tell() == s_len and not self.truncated: # At the end, return the last line if it wasn't truncated when reading it in. yield line
# Convenience wrappers around contents_header, shielding contents_header means we can # potentially do a better job lazy loading this data later on.
[docs] def search(self, pattern): return pattern.search(self.contents_header)
[docs] def search_str(self, query_str): return query_str in self.contents_header
[docs]def build_sniff_from_prefix(klass): # Build and attach a sniff function to this class (klass) from the sniff_prefix function # expected to be defined for the class. def auto_sniff(self, filename): file_prefix = FilePrefix(filename) datatype_compressed = getattr(self, "compressed", False) if file_prefix.compressed_format and not datatype_compressed: return False if datatype_compressed: if not file_prefix.compressed_format: # This not a compressed file we are looking but the type expects it to be # must return False. return False if hasattr(self, "compressed_format"): if self.compressed_format != file_prefix.compressed_format: return False return self.sniff_prefix(file_prefix) klass.sniff = auto_sniff return klass
[docs]def disable_parent_class_sniffing(klass): klass.sniff = lambda self, filename: False klass.sniff_prefix = lambda self, file_prefix: False return klass
[docs]def handle_compressed_file( filename, datatypes_registry, ext='auto', tmp_prefix='sniff_uncompress_', tmp_dir=None, in_place=False, check_content=True, auto_decompress=True, ): """ Check uploaded files for compression, check compressed file contents, and uncompress if necessary. Supports GZip, BZip2, and the first file in a Zip file. For performance reasons, the temporary file used for uncompression is located in the same directory as the input/output file. This behavior can be changed with the `tmp_dir` param. ``ext`` as returned will only be changed from the ``ext`` input param if the param was an autodetect type (``auto``) and the file was sniffed as a keep-compressed datatype. ``is_valid`` as returned will only be set if the file is compressed and contains invalid contents (or the first file in the case of a zip file), this is so lengthy decompression can be bypassed if there is invalid content in the first 32KB. Otherwise the caller should be checking content. """ CHUNK_SIZE = 2 ** 20 # 1Mb is_compressed = False compressed_type = None keep_compressed = False is_valid = False uncompressed = filename tmp_dir = tmp_dir or os.path.dirname(filename) for key, check_compressed_function in COMPRESSION_CHECK_FUNCTIONS: is_compressed, is_valid = check_compressed_function(filename, check_content=check_content) if is_compressed: compressed_type = key break # found compression type if is_compressed and is_valid: if ext in AUTO_DETECT_EXTENSIONS: # attempt to sniff for a keep-compressed datatype (observing the sniff order) sniff_datatypes = filter(lambda d: getattr(d, 'compressed', False), datatypes_registry.sniff_order) sniffed_ext = run_sniffers_raw(filename, sniff_datatypes) if sniffed_ext: ext = sniffed_ext keep_compressed = True else: datatype = datatypes_registry.get_datatype_by_extension(ext) keep_compressed = getattr(datatype, 'compressed', False) # don't waste time decompressing if we sniff invalid contents if is_compressed and is_valid and auto_decompress and not keep_compressed: fd, uncompressed = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir) compressed_file = DECOMPRESSION_FUNCTIONS[compressed_type](filename) # TODO: it'd be ideal to convert to posix newlines and space-to-tab here as well while True: try: chunk = compressed_file.read(CHUNK_SIZE) except OSError as e: os.close(fd) os.remove(uncompressed) compressed_file.close() raise OSError('Problem uncompressing {} data, please try retrieving the data uncompressed: {}'.format(compressed_type, util.unicodify(e))) if not chunk: break os.write(fd, chunk) os.close(fd) compressed_file.close() if in_place: # Replace the compressed file with the uncompressed file shutil.move(uncompressed, filename) uncompressed = filename elif not is_compressed or not check_content: is_valid = True return is_valid, ext, uncompressed, compressed_type
[docs]def handle_uploaded_dataset_file(*args, **kwds): """Legacy wrapper about handle_uploaded_dataset_file_internal for tools using it.""" return handle_uploaded_dataset_file_internal(*args, **kwds)[0]
[docs]def handle_uploaded_dataset_file_internal( filename, datatypes_registry, ext='auto', tmp_prefix='sniff_upload_', tmp_dir=None, in_place=False, check_content=True, is_binary=None, auto_decompress=True, uploaded_file_ext=None, convert_to_posix_lines=None, convert_spaces_to_tabs=None, ): is_valid, ext, converted_path, compressed_type = handle_compressed_file( filename, datatypes_registry, ext=ext, tmp_prefix=tmp_prefix, tmp_dir=tmp_dir, in_place=in_place, check_content=check_content, auto_decompress=auto_decompress, ) try: if not is_valid: if is_tar(converted_path): raise InappropriateDatasetContentError('TAR file uploads are not supported') raise InappropriateDatasetContentError('The uploaded compressed file contains invalid content') # This needs to be checked again after decompression is_binary = check_binary(converted_path) guessed_ext = ext if ext in AUTO_DETECT_EXTENSIONS: guessed_ext = guess_ext(converted_path, sniff_order=datatypes_registry.sniff_order, is_binary=is_binary) guessed_datatype = datatypes_registry.get_datatype_by_extension(guessed_ext) if not is_binary and guessed_datatype.is_binary: # It's possible to have a datatype that is binary but not within the first 1024 bytes, # so check_binary might return a false negative. This is for instance true for PDF files is_binary = True if not is_binary and (convert_to_posix_lines or convert_spaces_to_tabs): # Convert universal line endings to Posix line endings, spaces to tabs (if desired) if convert_spaces_to_tabs: convert_fxn = convert_newlines_sep2tabs else: convert_fxn = convert_newlines line_count, _converted_path = convert_fxn(converted_path, in_place=in_place, tmp_dir=tmp_dir, tmp_prefix=tmp_prefix) if not in_place: if converted_path and filename != converted_path: os.unlink(converted_path) converted_path = _converted_path if ext in AUTO_DETECT_EXTENSIONS: ext = guess_ext(converted_path, sniff_order=datatypes_registry.sniff_order, is_binary=is_binary) else: ext = guessed_ext if not is_binary and check_content and check_html(converted_path): raise InappropriateDatasetContentError('The uploaded file contains invalid HTML content') except Exception: if filename != converted_path: os.unlink(converted_path) raise return ext, converted_path, compressed_type
AUTO_DETECT_EXTENSIONS = ['auto'] # should 'data' also cause auto detect? DECOMPRESSION_FUNCTIONS = dict(gz=gzip.GzipFile, bz2=bz2.BZ2File, zip=zip_single_fileobj) COMPRESSION_CHECK_FUNCTIONS = [('gz', check_gzip), ('bz2', check_bz2), ('zip', check_zip)]
[docs]class InappropriateDatasetContentError(Exception): pass
if __name__ == '__main__': import doctest doctest.testmod(sys.modules[__name__])