/usr/lib/python2.7/dist-packages/neo/test/iotest/common_io_test.py is in python-neo 0.3.3-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | # -*- coding: utf-8 -*-
'''
Common tests for IOs:
* check presence of all necessary attr
* check types
* write/read consistency
See BaseTestIO.
The public URL is in url_for_tests.
The private url for writing is
ssh://gate.g-node.org/groups/neo/io_test_files/
'''
# needed for python 3 compatibility
from __future__ import absolute_import
__test__ = False
url_for_tests = "https://portal.g-node.org/neo/"
import os
try:
import unittest2 as unittest
except ImportError:
import unittest
from neo.core import Block, Segment
from neo.test.tools import (assert_same_sub_schema,
assert_neo_object_is_compliant,
assert_sub_schema_is_lazy_loaded,
assert_lazy_sub_schema_can_be_loaded,
assert_children_empty)
from neo.test.iotest.tools import (can_use_network, cleanup_test_file,
close_object_safe, create_generic_io_object,
create_generic_reader, create_generic_writer,
create_local_temp_dir, download_test_file,
iter_generic_io_objects,
iter_generic_readers, iter_read_objects,
make_all_directories, read_generic,
write_generic)
from neo.test.iotest.generate_datasets import generate_from_supported_objects
class BaseTestIO(object):
'''
This class make common tests for all IOs.
Several startegies:
* for IO able to read write : test_write_then_read
* for IO able to read write with hash conservation (optional):
test_read_then_write
* for all IOs : test_assert_readed_neo_object_is_compliant
2 cases:
* files are at G-node and downloaded:
download_test_files_if_not_present
* files are generated by MyIO.write()
'''
#~ __test__ = False
# all IO test need to modify this:
ioclass = None # the IOclass to be tested
files_to_test = [] # list of files to test compliances
files_to_download = [] # when files are at G-Node
# when reading then writing produces files with identical hashes
hash_conserved_when_write_read = False
# when writing then reading creates an identical neo object
read_and_write_is_bijective = True
# allow environment to tell avoid using network
use_network = can_use_network()
local_test_dir = None
def setUp(self):
'''
Set up the test fixture. This is run for every test
'''
self.higher = self.ioclass.supported_objects[0]
self.shortname = self.ioclass.__name__.lower().strip('io')
# these objects can both be written and read
self.io_readandwrite = list(set(self.ioclass.readable_objects) &
set(self.ioclass.writeable_objects))
# these objects can be either written or read
self.io_readorwrite = list(set(self.ioclass.readable_objects) |
set(self.ioclass.writeable_objects))
self.create_local_dir_if_not_exists()
self.download_test_files_if_not_present()
self.files_generated = []
self.generate_files_for_io_able_to_write()
self.files_to_test.extend(self.files_generated)
self.cascade_modes = [True]
if hasattr(self.ioclass, 'load_lazy_cascade'):
self.cascade_modes.append('lazy')
def create_local_dir_if_not_exists(self):
'''
Create a local directory to store testing files and return it.
The directory path is also written to self.local_test_dir
'''
self.local_test_dir = create_local_temp_dir(self.shortname)
return self.local_test_dir
def download_test_files_if_not_present(self):
'''
Download %s file at G-node for testing
url_for_tests is global at beginning of this file.
''' % self.ioclass.__name__
if not self.use_network:
raise unittest.SkipTest("Requires download of data from the web")
url = url_for_tests+self.shortname
try:
make_all_directories(self.files_to_download, self.local_test_dir)
download_test_file(self.files_to_download,
self.local_test_dir, url)
except IOError as exc:
raise unittest.SkipTest(exc)
download_test_files_if_not_present.__test__ = False
def cleanup_file(self, path):
'''
Remove test files or directories safely.
'''
cleanup_test_file(self.ioclass, path, directory=self.local_test_dir)
def able_to_write_or_read(self, writeread=False, readwrite=False):
'''
Return True if generalized writing or reading is possible.
If writeread=True, return True if writing then reading is
possible and produces identical neo objects.
If readwrite=True, return True if reading then writing is possible
and produces files with identical hashes.
'''
# Find the highest object that is supported by the IO
# Test only if it is a Block or Segment, and if it can both read
# and write this object.
if self.higher not in self.io_readandwrite:
return False
if self.higher not in [Block, Segment]:
return False
# when io need external knowldge for writting or read such as
# sampling_rate (RawBinaryIO...) the test is too much complex to design
# genericaly.
if (self.higher in self.ioclass.read_params and
len(self.ioclass.read_params[self.higher]) != 0):
return False
# handle cases where the test should write then read
if writeread and not self.read_and_write_is_bijective:
return False
# handle cases where the test should read then write
if readwrite and not self.hash_conserved_when_write_read:
return False
return True
def get_filename_path(self, filename):
'''
Get the path to a filename in the current temporary file directory
'''
return os.path.join(self.local_test_dir, filename)
def generic_io_object(self, filename=None, return_path=False, clean=False):
'''
Create an io object in a generic way that can work with both
file-based and directory-based io objects.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the io object. return ioobj, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
'''
return create_generic_io_object(ioclass=self.ioclass,
filename=filename,
directory=self.local_test_dir,
return_path=return_path,
clean=clean)
def create_file_reader(self, filename=None, return_path=False,
clean=False, target=None, readall=False):
'''
Create a function that can read from the specified filename.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the reader function. return reader, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If target is None, use the first supported_objects from ioobj
If target is False, use the 'read' method.
If target is the Block or Segment class, use read_block or
read_segment, respectively.
If target is a string, use 'read_'+target.
If readall is True, use the read_all_ method instead of the read_
method. Default is False.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True, clean=clean)
res = create_generic_reader(ioobj, target=target, readall=readall)
if return_path:
return res, path
return res
def create_file_writer(self, filename=None, return_path=False,
clean=False, target=None):
'''
Create a function that can write from the specified filename.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the writer function. return writer, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If target is None, use the first supported_objects from ioobj
If target is False, use the 'write' method.
If target is the Block or Segment class, use write_block or
write_segment, respectively.
If target is a string, use 'write_'+target.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True, clean=clean)
res = create_generic_writer(ioobj, target=target)
if return_path:
return res, path
return res
def read_file(self, filename=None, return_path=False, clean=False,
target=None, readall=False, cascade=True, lazy=False):
'''
Read from the specified filename.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the object. return obj, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If target is None, use the first supported_objects from ioobj
If target is False, use the 'read' method.
If target is the Block or Segment class, use read_block or
read_segment, respectively.
If target is a string, use 'read_'+target.
The cascade and lazy parameters are passed to the reader. Defaults
are True and False, respectively.
If readall is True, use the read_all_ method instead of the read_
method. Default is False.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True, clean=clean)
obj = read_generic(ioobj, target=target, cascade=cascade, lazy=lazy,
readall=readall, return_reader=False)
if return_path:
return obj, path
return obj
def write_file(self, obj=None, filename=None, return_path=False,
clean=False, target=None):
'''
Write the target object to a file using the given neo io object ioobj.
If filename is None, create a filename (default).
If return_path is True, return the full path of the file along with
the object. return obj, path. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If target is None, use the first supported_objects from ioobj
If target is False, use the 'read' method.
If target is the Block or Segment class, use read_block or
read_segment, respectively.
If target is a string, use 'read_'+target.
obj is the object to write. If obj is None, an object is created
automatically for the io class.
'''
ioobj, path = self.generic_io_object(filename=filename,
return_path=True, clean=clean)
obj = write_generic(ioobj, target=target, return_reader=False)
if return_path:
return obj, path
return obj
def iter_io_objects(self, return_path=False, clean=False):
'''
Return an iterable over the io objects created from files_to_test
If return_path is True, yield the full path of the file along with
the io object. yield ioobj, path Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
'''
return iter_generic_io_objects(ioclass=self.ioclass,
filenames=self.files_to_test,
directory=self.local_test_dir,
return_path=return_path,
clean=clean)
def iter_readers(self, target=None, readall=False,
return_path=False, return_ioobj=False, clean=False):
'''
Return an iterable over readers created from files_to_test.
If return_path is True, return the full path of the file along with
the reader object. return reader, path.
If return_ioobj is True, return the io object as well as the reader.
return reader, ioobj. Default is False.
If both return_path and return_ioobj is True,
return reader, path, ioobj. Default is False.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
If readall is True, use the read_all_ method instead of the
read_ method. Default is False.
'''
return iter_generic_readers(ioclass=self.ioclass,
filenames=self.files_to_test,
directory=self.local_test_dir,
return_path=return_path,
return_ioobj=return_ioobj,
target=target,
clean=clean,
readall=readall)
def iter_objects(self, target=None, return_path=False, return_ioobj=False,
return_reader=False, clean=False, readall=False,
cascade=True, lazy=False):
'''
Iterate over objects read from the list of filenames in files_to_test.
If target is None, use the first supported_objects from ioobj
If target is False, use the 'read' method.
If target is the Block or Segment class, use read_block or
read_segment, respectively.
If target is a string, use 'read_'+target.
If return_path is True, yield the full path of the file along with
the object. yield obj, path.
If return_ioobj is True, yield the io object as well as the object.
yield obj, ioobj. Default is False.
If return_reader is True, yield the io reader function as well as the
object. yield obj, reader. Default is False.
If some combination of return_path, return_ioobj, and return_reader
is True, they are yielded in the order: obj, path, ioobj, reader.
If clean is True, try to delete existing versions of the file
before creating the io object. Default is False.
The cascade and lazy parameters are passed to the reader. Defaults
are True and False, respectively.
If readall is True, use the read_all_ method instead of the read_
method. Default is False.
'''
return iter_read_objects(ioclass=self.ioclass,
filenames=self.files_to_test,
directory=self.local_test_dir,
target=target,
return_path=return_path,
return_ioobj=return_ioobj,
return_reader=return_reader,
clean=clean, readall=readall,
cascade=cascade, lazy=lazy)
def generate_files_for_io_able_to_write(self):
'''
Write files for use in testing.
'''
self.files_generated = []
if not self.able_to_write_or_read():
return
generate_from_supported_objects(self.ioclass.supported_objects)
ioobj, path = self.generic_io_object(return_path=True, clean=True)
if ioobj is None:
return
self.files_generated.append(path)
write_generic(ioobj, target=self.higher)
close_object_safe(ioobj)
def test_write_then_read(self):
'''
Test for IO that are able to write and read - here %s:
1 - Generate a full schema with supported objects.
2 - Write to a file
3 - Read from the file
4 - Check the hierachy
5 - Check data
Work only for IO for Block and Segment for the highest object
(main cases).
''' % self.ioclass.__name__
if not self.able_to_write_or_read(writeread=True):
return
for cascade in self.cascade_modes:
ioobj1 = self.generic_io_object(clean=True)
if ioobj1 is None:
return
ob1 = write_generic(ioobj1, target=self.higher)
close_object_safe(ioobj1)
ioobj2 = self.generic_io_object()
# Read the highest supported object from the file
obj_reader = create_generic_reader(ioobj2, target=False)
ob2 = obj_reader(cascade=cascade)[0]
if self.higher == Segment:
ob2 = ob2.segments[0]
# some formats (e.g. elphy) do not support double floating
# point spiketrains
try:
assert_same_sub_schema(ob1, ob2, False, 1e-8)
assert_neo_object_is_compliant(ob1)
assert_neo_object_is_compliant(ob2)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('with cascade=%s ' % cascade,)
raise
close_object_safe(ioobj2)
def test_read_then_write(self):
'''
Test for IO that are able to read and write, here %s:
1 - Read a file
2 Write object set in another file
3 Compare the 2 files hash
NOTE: TODO: Not implemented yet
''' % self.ioclass.__name__
if not self.able_to_write_or_read(readwrite=True):
return
#assert_file_contents_equal(a, b)
def test_assert_readed_neo_object_is_compliant(self):
'''
Reading %s files in `files_to_test` produces compliant objects.
Compliance test: neo.test.tools.assert_neo_object_is_compliant for
all cascade and lazy modes
''' % self.ioclass.__name__
# This is for files presents at G-Node or generated
for cascade in self.cascade_modes:
for lazy in [True, False]:
for obj, path in self.iter_objects(cascade=cascade, lazy=lazy,
return_path=True):
try:
# Check compliance of the block
assert_neo_object_is_compliant(obj)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s with cascade=%s and lazy=%s' %
(os.path.basename(path), cascade, lazy),)
raise
def test_readed_with_cascade_is_compliant(self):
'''
Reading %s files in `files_to_test` with `cascade` is compliant.
A reader with cascade = False should return empty children.
''' % self.ioclass.__name__
# This is for files presents at G-Node or generated
for obj, path in self.iter_objects(cascade=False, lazy=False,
return_path=True):
try:
# Check compliance of the block or segment
assert_neo_object_is_compliant(obj)
assert_children_empty(obj, self.ioclass)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s ' % os.path.basename(path),)
raise
def test_readed_with_lazy_is_compliant(self):
'''
Reading %s files in `files_to_test` with `lazy` is compliant.
Test the reader with lazy = True. All objects derived from ndarray
or Quantity should have a size of 0. Also, AnalogSignal,
AnalogSignalArray, SpikeTrain, Epocharray, and EventArray should
contain the lazy_shape attribute.
''' % self.ioclass.__name__
# This is for files presents at G-Node or generated
for cascade in self.cascade_modes:
for obj, path in self.iter_objects(cascade=cascade, lazy=True,
return_path=True):
try:
assert_sub_schema_is_lazy_loaded(obj)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s with cascade=%s ' %
(os.path.basename(path), cascade),)
raise
def test_load_lazy_objects(self):
'''
Reading %s files in `files_to_test` with `lazy` works.
Test the reader with lazy = True. All objects derived from ndarray
or Quantity should have a size of 0. Also, AnalogSignal,
AnalogSignalArray, SpikeTrain, Epocharray, and EventArray should
contain the lazy_shape attribute.
''' % self.ioclass.__name__
if not hasattr(self.ioclass, 'load_lazy_object'):
return
# This is for files presents at G-Node or generated
for cascade in self.cascade_modes:
for obj, path, ioobj in self.iter_objects(cascade=cascade,
lazy=True,
return_ioobj=True,
return_path=True):
try:
assert_lazy_sub_schema_can_be_loaded(obj, ioobj)
# intercept exceptions and add more information
except BaseException as exc:
exc.args += ('from %s with cascade=%s ' %
(os.path.basename(path), cascade),)
raise
|