def test_call_variants_with_empty_input(self):
source_path = test_utils.test_tmpfile('empty.tfrecord')
io_utils.write_tfrecords([], source_path)
# Make sure that prepare_inputs don't crash on empty input.
call_variants.prepare_inputs(source_path,
modeling.get_model('random_guess'),
batch_size=1)
def test_call_variants_with_no_shape(self, model):
# Read one good record from a valid file.
example = next(io_utils.read_tfrecords(testdata.GOLDEN_CALLING_EXAMPLES))
# Remove image/shape.
del example.features.feature['image/shape']
source_path = test_utils.test_tmpfile('make_examples_out_noshape.tfrecord')
io_utils.write_tfrecords([example], source_path)
with self.assertRaisesRegexp(
ValueError, 'Invalid image/shape: we expect to find an image/shape '
'field with length 3.'):
call_variants.prepare_inputs(source_path, model, batch_size=1)
def test_call_variants_with_no_shape(self, model):
# Read one good record from a valid file.
example = next(io_utils.read_tfrecords(test_utils.GOLDEN_CALLING_EXAMPLES))
# Remove image/shape.
del example.features.feature['image/shape']
source_path = test_utils.test_tmpfile('make_examples_out_noshape.tfrecord')
io_utils.write_tfrecords([example], source_path)
with self.assertRaisesRegexp(
ValueError, 'Invalid image/shape: we expect to find an image/shape '
'field with length 3.'):
call_variants.prepare_inputs(source_path, model, batch_size=1)
def test_prepare_inputs(self, filename_to_write, file_string_input):
source_path = test_utils.test_tmpfile(filename_to_write)
io_utils.write_tfrecords(self.examples, source_path)
# file_string_input could be a comma-separated list. Add the prefix to all
# of them, and join it back to a string.
file_string_input = ','.join(
[test_utils.test_tmpfile(f) for f in file_string_input.split(',')])
with self.test_session() as sess:
sess.run(tf.local_variables_initializer())
sess.run(tf.global_variables_initializer())
ds = call_variants.prepare_inputs(file_string_input)
_, variants, _ = data_providers.get_infer_batches(ds,
model=self.model,
batch_size=1)
seen_variants = []
try:
while True:
seen_variants.extend(sess.run(variants))
except tf.errors.OutOfRangeError:
pass
self.assertItemsEqual(self.variants,
variant_utils.decode_variants(seen_variants))
def test_prepare_inputs(self, filename, expand_to_file_pattern):
source_path = test_utils.test_tmpfile(filename)
io_utils.write_tfrecords(self.examples, source_path)
if expand_to_file_pattern:
# Transform foo@3 to foo-?????-of-00003.
source_path = io_utils.NormalizeToShardedFilePattern(source_path)
with self.test_session() as sess:
sess.run(tf.local_variables_initializer())
sess.run(tf.global_variables_initializer())
ds = call_variants.prepare_inputs(source_path)
_, variants, _ = data_providers.get_infer_batches(ds,
model=self.model,
batch_size=1)
seen_variants = []
try:
while True:
seen_variants.extend(sess.run(variants))
except tf.errors.OutOfRangeError:
pass
self.assertItemsEqual(self.variants,
variant_utils.decode_variants(seen_variants))
def test_call_variants_with_no_shape(self, model):
# Read one good record from a valid file.
example = next(tfrecord.read_tfrecords(testdata.GOLDEN_CALLING_EXAMPLES))
# Remove image/shape.
del example.features.feature['image/shape']
source_path = test_utils.test_tmpfile('make_examples_out_noshape.tfrecord')
tfrecord.write_tfrecords([example], source_path)
with six.assertRaisesRegex(
self, ValueError,
'Invalid image/shape: we expect to find an image/shape '
'field with length 3.'):
ds = call_variants.prepare_inputs(source_path)
_ = list(data_providers.get_infer_batches(ds, model=model, batch_size=1))
def test_call_variants_with_empty_input(self):
source_path = test_utils.test_tmpfile('empty.tfrecord')
tfrecord.write_tfrecords([], source_path)
# Make sure that prepare_inputs don't crash on empty input.
ds = call_variants.prepare_inputs(source_path)
m = modeling.get_model('random_guess')
# The API specifies that OutOfRangeError is thrown in this case.
batches = list(_get_infer_batches(ds, model=m, batch_size=1))
with self.test_session() as sess:
sess.run(tf.compat.v1.local_variables_initializer())
sess.run(tf.compat.v1.global_variables_initializer())
try:
_ = sess.run(batches)
except tf.errors.OutOfRangeError:
pass
def test_prepare_inputs(self, filename, expand_to_file_pattern):
source_path = test_utils.test_tmpfile(filename)
io_utils.write_tfrecords(self.examples, source_path)
if expand_to_file_pattern:
# Transform foo@3 to foo-?????-of-00003.
source_path = io_utils.NormalizeToShardedFilePattern(source_path)
with self.test_session() as sess:
_, variants, _ = call_variants.prepare_inputs(
source_path, self.model, batch_size=1)
sess.run(tf.local_variables_initializer())
sess.run(tf.global_variables_initializer())
seen_variants = []
try:
while True:
seen_variants.extend(sess.run(variants))
except tf.errors.OutOfRangeError:
pass
self.assertItemsEqual(self.variants,
variant_utils.decode_variants(seen_variants))
def test_call_variants_with_empty_input(self):
source_path = test_utils.test_tmpfile('empty.tfrecord')
io_utils.write_tfrecords([], source_path)
# Make sure that prepare_inputs don't crash on empty input.
call_variants.prepare_inputs(
source_path, modeling.get_model('random_guess'), batch_size=1)
