def test_convert_newlines_non_utf(): fname = get_test_fname("dosimzml") rval = convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir(), in_place=False) new_file = rval[1] assert open(new_file, "rb").read() == open(get_test_fname("1imzml"), "rb").read()
def test_sniff_compressed_dynamic_datatypes_default_on(): # With auto sniffing on, verify the sniffers work and the files match what is expected # when coming from guess_ext. datatypes_registry = example_datatype_registry_for_sample(sniff_compressed_dynamic_datatypes_default=True) fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension('fastqsanger.gz') fname = sniff.get_test_fname('1.fastqsanger.gz') assert fastqsangergz_datatype.sniff(fname) sniff_order = datatypes_registry.sniff_order fname = sniff.get_test_fname('1.fastqsanger.gz') assert sniff.guess_ext(fname, sniff_order) == 'fastqsanger.gz' fname = sniff.get_test_fname('1.fastqsanger.bz2') assert sniff.guess_ext(fname, sniff_order) == 'fastqsanger.bz2'
def test_sniff_compressed_dynamic_datatypes_default_off(): # Redo last tests with auto compressed sniffing disabled and they should not longer result from guess_ext. datatypes_registry = example_datatype_registry_for_sample(sniff_compressed_dynamic_datatypes_default=False) # sniffer still returns True for these files... fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension('fastqsanger.gz') fname = sniff.get_test_fname('1.fastqsanger.gz') assert fastqsangergz_datatype.sniff(fname) # but they don't report as matching the specified sniff_order. sniff_order = datatypes_registry.sniff_order fname = sniff.get_test_fname('1.fastqsanger.gz') assert 'fastq' not in sniff.guess_ext(fname, sniff_order) fname = sniff.get_test_fname('1.fastqsanger.bz2') assert 'fastq' not in sniff.guess_ext(fname, sniff_order)
def test_sniff_compressed_dynamic_datatypes_default_on(): # With auto sniffing on, verify the sniffers work and the files match what is expected # when coming from guess_ext. datatypes_registry = example_datatype_registry_for_sample( sniff_compressed_dynamic_datatypes_default=True) fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension( 'fastqsanger.gz') fname = sniff.get_test_fname('1.fastqsanger.gz') assert fastqsangergz_datatype.sniff(fname) sniff_order = datatypes_registry.sniff_order fname = sniff.get_test_fname('1.fastqsanger.gz') assert sniff.guess_ext(fname, sniff_order) == 'fastqsanger.gz' fname = sniff.get_test_fname('1.fastqsanger.bz2') assert sniff.guess_ext(fname, sniff_order) == 'fastqsanger.bz2'
def test_sniff_compressed_dynamic_datatypes_default_off(): # Redo last tests with auto compressed sniffing disabled and they should not longer result from guess_ext. datatypes_registry = example_datatype_registry_for_sample( sniff_compressed_dynamic_datatypes_default=False) # sniffer still returns True for these files... fastqsangergz_datatype = datatypes_registry.get_datatype_by_extension( 'fastqsanger.gz') fname = sniff.get_test_fname('1.fastqsanger.gz') assert fastqsangergz_datatype.sniff(fname) # but they don't report as matching the specified sniff_order. sniff_order = datatypes_registry.sniff_order fname = sniff.get_test_fname('1.fastqsanger.gz') assert 'fastq' not in sniff.guess_ext(fname, sniff_order) fname = sniff.get_test_fname('1.fastqsanger.bz2') assert 'fastq' not in sniff.guess_ext(fname, sniff_order)
def assert_converts_to_1234_convert(content, block_size=1024): fname = get_test_fname('temp2.txt') with open(fname, 'w') as fh: fh.write(content) rval = convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir(), block_size=block_size) actual_contents = open(fname).read() assert '1 2\n3 4\n' == actual_contents, actual_contents assert rval == (2, None), "rval != %s for %s" % (rval, content)
def get_input_files(*args): temp_dir = tempfile.mkdtemp() test_files = [] try: for filename in args: shutil.copy(get_test_fname(filename), temp_dir) test_files.append(os.path.join(temp_dir, filename)) md5_sums = [md5_hash_file(f) for f in test_files] yield test_files new_md5_sums = [md5_hash_file(f) for f in test_files] for old_hash, new_hash, f in zip(md5_sums, new_md5_sums, test_files): assert old_hash == new_hash, 'Unexpected change of content for file %s' % f finally: shutil.rmtree(temp_dir, ignore_errors=True)
if line.lstrip().startswith('</cml>'): continue if line.lstrip().startswith('<molecule'): molecule_found = True if molecule_found: out.write(line) out.write("</cml>\n") merge = staticmethod(merge) if __name__ == '__main__': """ TODO: We need to figure out, how to put example files under /lib/galaxy/datatypes/test/ from a toolshed, so that doctest can work properly. """ inchi = get_test_fname('drugbank_drugs.inchi') smiles = get_test_fname('drugbank_drugs.smi') sdf = get_test_fname('drugbank_drugs.sdf') fps = get_test_fname('50_chemfp_fingerprints_FPS1.fps') pdb = get_test_fname('2zbz.pdb') cml = get_test_fname('/home/bag/Downloads/approved.cml') print 'CML test' print CML().sniff(cml), 'cml' print CML().sniff(inchi) print CML().sniff(pdb) CML().split() """ print 'SMILES test' print SMILES().sniff(smiles), 'smi' print SMILES().sniff(inchi)
# we found two required header lines, the next line should start with <molecule > if line.lstrip().startswith('</cml>'): continue if line.lstrip().startswith('<molecule'): molecule_found = True if molecule_found: out.write( line ) out.write("</cml>\n") merge = staticmethod(merge) if __name__ == '__main__': """ TODO: We need to figure out, how to put example files under /lib/galaxy/datatypes/test/ from a toolshed, so that doctest can work properly. """ inchi = get_test_fname('drugbank_drugs.inchi') smiles = get_test_fname('drugbank_drugs.smi') sdf = get_test_fname('drugbank_drugs.sdf') fps = get_test_fname('50_chemfp_fingerprints_FPS1.fps') pdb = get_test_fname('2zbz.pdb') cml = get_test_fname('/home/bag/Downloads/approved.cml') print 'CML test' print CML().sniff(cml), 'cml' print CML().sniff(inchi) print CML().sniff(pdb) CML().split() """ print 'SMILES test' print SMILES().sniff(smiles), 'smi' print SMILES().sniff(inchi)
def _run_validation(extension, file_name): datatype = datatypes_registry.datatypes_by_extension[extension] validation = validate(MockDataset(get_test_fname(file_name), datatype)) return validation
def _truncate(file_name, bytes=10): o = tempfile.NamedTemporaryFile(delete=False) with open(get_test_fname(file_name), "rb") as f: contents = f.read() o.write(contents[0:-bytes]) return o.name