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# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2014-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
"""
Tests for various argument-handling code.
"""
from __future__ import print_function, unicode_literals
from __future__ import absolute_import
import sys
import io
import collections
from . import khmer_tst_utils as utils
import argparse
import khmer.kfile
from khmer import khmer_args
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
import sys
# For map(long, [list of ints]) cross-version hackery
if sys.version_info.major > 2:
long = int
def test_check_space():
fakelump_fa = utils.get_test_data('fakelump.fa')
save_stderr, sys.stderr = sys.stderr, io.StringIO()
try:
khmer.kfile.check_space(
[fakelump_fa], force=False, _testhook_free_space=0)
assert 0, "this should fail"
except SystemExit as e:
print(str(e))
finally:
sys.stderr = save_stderr
def test_check_tablespace():
outfile = utils.get_test_data('truncated.fq')
save_stderr, sys.stderr = sys.stderr, io.StringIO()
parser = khmer_args.build_counting_args()
args = parser.parse_args(['-M', '1e9'])
try:
tablesize = khmer_args.calculate_graphsize(args, 'countgraph')
khmer.kfile.check_space_for_graph(outfile, tablesize,
False, _testhook_free_space=0)
assert 0, "this should fail"
except SystemExit as e:
print(str(e))
finally:
sys.stderr = save_stderr
def test_check_space_force():
fakelump_fa = utils.get_test_data('fakelump.fa')
save_stderr, sys.stderr = sys.stderr, io.StringIO()
try:
khmer.kfile.check_space(
[fakelump_fa], force=True, _testhook_free_space=0)
assert True, "this should pass"
except SystemExit as e:
print(str(e))
finally:
sys.stderr = save_stderr
def test_check_tablespace_force():
save_stderr, sys.stderr = sys.stderr, io.StringIO()
outfile = utils.get_test_data('truncated')
parser = khmer_args.build_counting_args()
args = parser.parse_args(['-M', '1e9'])
try:
tablesize = khmer_args.calculate_graphsize(args, 'countgraph')
khmer.kfile.check_space_for_graph(outfile, tablesize,
True, _testhook_free_space=0)
assert True, "this should pass"
except SystemExit as e:
print(str(e))
finally:
sys.stderr = save_stderr
def test_invalid_file_warn():
save_stderr, sys.stderr = sys.stderr, io.StringIO()
try:
khmer.kfile.check_valid_file_exists(["nonexistent", "nonexistent2"])
assert sys.stderr.getvalue().count("\n") == 2, \
"Should produce two warning lines"
except SystemExit as e:
print(str(e))
finally:
sys.stderr = save_stderr
def test_check_valid_stdin_nowarn():
save_stderr, sys.stderr = sys.stderr, io.StringIO()
try:
khmer.kfile.check_valid_file_exists(["-"])
err = sys.stderr.getvalue()
assert err.count("\n") == 0, err
except SystemExit as e:
print(str(e))
finally:
sys.stderr = save_stderr
FakeArgparseObject = collections.namedtuple('FakeArgs',
['ksize', 'n_tables',
'max_tablesize',
'max_memory_usage',
'unique_kmers'])
def test_create_countgraph_1():
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
countgraph = khmer_args.create_countgraph(args)
expected_hashsz = utils.longify([2499997, 2499989, 2499983, 2499967])
assert countgraph.hashsizes() == expected_hashsz, countgraph.hashsizes()
assert sum(countgraph.hashsizes()) < max_mem, sum(countgraph.hashsizes())
def test_create_countgraph_2():
# tests overriding ksize by passing into create_nodegraph explicitly.
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
countgraph = khmer_args.create_countgraph(args, ksize=15)
assert countgraph.ksize() == 15
def test_create_countgraph_3():
# tests too-big ksize
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
old_stderr = sys.stderr
sys.stderr = capture = StringIO()
try:
countgraph = khmer_args.create_countgraph(args, ksize=35)
assert 0, "should not reach this"
except SystemExit:
err = capture.getvalue()
assert 'khmer only supports k-mer sizes <= 32.' in err, err
finally:
sys.stderr = old_stderr
def test_create_countgraph_4_multiplier():
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
countgraph = khmer_args.create_countgraph(args, multiplier=2.0)
assert sum(countgraph.hashsizes()) < max_mem / 2.0, \
sum(countgraph.hashsizes())
def test_create_nodegraph_1():
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
nodegraph = khmer_args.create_nodegraph(args)
expected_hashsz = utils.longify([19999999, 19999981, 19999963, 19999927])
assert nodegraph.hashsizes() == expected_hashsz, nodegraph.hashsizes()
assert sum(nodegraph.hashsizes()) / \
8.0 < max_mem, sum(nodegraph.hashsizes())
def test_create_nodegraph_2():
# tests overriding ksize by passing into create_nodegraph explicitly.
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
nodegraph = khmer_args.create_nodegraph(args, ksize=15)
assert nodegraph.ksize() == 15
def test_create_nodegraph_3():
# tests too-big ksize
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
old_stderr = sys.stderr
sys.stderr = capture = StringIO()
try:
nodegraph = khmer_args.create_nodegraph(args, ksize=35)
assert 0, "should not reach this"
except SystemExit:
err = capture.getvalue()
assert 'khmer only supports k-mer sizes <= 32.' in err, err
def test_create_nodegraph_4_multiplier():
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
nodegraph = khmer_args.create_nodegraph(args, multiplier=2.0)
assert sum(nodegraph.hashsizes()) / 8.0 < max_mem / 2.0, \
sum(nodegraph.hashsizes())
def test_report_on_config_bad_graphtype():
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
try:
khmer_args.report_on_config(args, 'foograph')
assert 0, "the previous statement should raise an exception"
except ValueError as err:
assert "unknown graph type: foograph" in str(err), str(err)
def test_fail_calculate_foograph_size():
# tests unknown graph type
ksize = khmer_args.DEFAULT_K
n_tables = khmer_args.DEFAULT_N_TABLES
max_tablesize = khmer_args.DEFAULT_MAX_TABLESIZE
max_mem = 1e7
args = FakeArgparseObject(ksize, n_tables, max_tablesize, max_mem, 0)
try:
nodegraph = khmer_args.calculate_graphsize(args, 'foograph')
assert 0, "previous statement should fail"
except ValueError as err:
assert "unknown graph type: foograph" in str(err), str(err)
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