def test_print_info(self):
db_file = 'foo'
self.assertRaises(InfoSystemExit, print_info, 'object', db_file)
db_file = os.path.join(self.testdir, './acct.db')
self.assertRaises(InfoSystemExit, print_info, 'account', db_file)
controller = AccountController({
'devices': self.testdir,
'mount_check': 'false'
})
req = Request.blank('/sda1/1/acct',
environ={
'REQUEST_METHOD': 'PUT',
'HTTP_X_TIMESTAMP': '0'
})
resp = req.get_response(controller)
self.assertEqual(resp.status_int, 201)
out = StringIO()
exp_raised = False
with mock.patch('sys.stdout', out):
db_file = os.path.join(self.testdir, 'sda1', 'accounts', '1',
'b47', 'dc5be2aa4347a22a0fee6bc7de505b47',
'dc5be2aa4347a22a0fee6bc7de505b47.db')
try:
print_info('account', db_file, swift_dir=self.testdir)
except Exception:
exp_raised = True
if exp_raised:
self.fail("Unexpected exception raised")
else:
self.assertTrue(len(out.getvalue().strip()) > 800)
controller = ContainerController({
'devices': self.testdir,
'mount_check': 'false'
})
req = Request.blank('/sda1/1/acct/cont',
environ={
'REQUEST_METHOD': 'PUT',
'HTTP_X_TIMESTAMP': '0'
})
resp = req.get_response(controller)
self.assertEqual(resp.status_int, 201)
out = StringIO()
exp_raised = False
with mock.patch('sys.stdout', out):
db_file = os.path.join(self.testdir, 'sda1', 'containers', '1',
'cae', 'd49d0ecbb53be1fcc49624f2f7c7ccae',
'd49d0ecbb53be1fcc49624f2f7c7ccae.db')
orig_cwd = os.getcwd()
try:
os.chdir(os.path.dirname(db_file))
print_info('container',
os.path.basename(db_file),
swift_dir='/dev/null')
except Exception:
exp_raised = True
finally:
os.chdir(orig_cwd)
if exp_raised:
self.fail("Unexpected exception raised")
else:
self.assertTrue(len(out.getvalue().strip()) > 600)
out = StringIO()
exp_raised = False
with mock.patch('sys.stdout', out):
db_file = os.path.join(self.testdir, 'sda1', 'containers', '1',
'cae', 'd49d0ecbb53be1fcc49624f2f7c7ccae',
'd49d0ecbb53be1fcc49624f2f7c7ccae.db')
orig_cwd = os.getcwd()
try:
os.chdir(os.path.dirname(db_file))
print_info('account',
os.path.basename(db_file),
swift_dir='/dev/null')
except InfoSystemExit:
exp_raised = True
finally:
os.chdir(orig_cwd)
if exp_raised:
exp_out = 'Does not appear to be a DB of type "account":' \
' ./d49d0ecbb53be1fcc49624f2f7c7ccae.db'
self.assertEqual(out.getvalue().strip(), exp_out)
else:
self.fail("Expected an InfoSystemExit exception to be raised")
def reset(self):
self.out = StringIO()
self.messages = []
def str_diagnostic(expected, value, rtol, atol):
"""Return a pretty multiline string representating the cause
of the exception"""
sio = StringIO()
try:
ssio = StringIO()
print(" : shape, dtype, strides, min, max, n_inf, n_nan:",
file=ssio)
print(" Expected :", end=' ', file=ssio)
print(expected.shape, end=' ', file=ssio)
print(expected.dtype, end=' ', file=ssio)
print(expected.strides, end=' ', file=ssio)
print(expected.min(), end=' ', file=ssio)
print(expected.max(), end=' ', file=ssio)
print(np.isinf(expected).sum(), end=' ', file=ssio)
print(np.isnan(expected).sum(), end=' ', file=ssio)
# only if all succeeds to we add anything to sio
print(ssio.getvalue(), file=sio)
except Exception:
pass
try:
ssio = StringIO()
print(" Value :", end=' ', file=ssio)
print(value.shape, end=' ', file=ssio)
print(value.dtype, end=' ', file=ssio)
print(value.strides, end=' ', file=ssio)
print(value.min(), end=' ', file=ssio)
print(value.max(), end=' ', file=ssio)
print(np.isinf(value).sum(), end=' ', file=ssio)
print(np.isnan(value).sum(), end=' ', file=ssio)
# only if all succeeds to we add anything to sio
print(ssio.getvalue(), file=sio)
except Exception:
pass
print(" expected :", expected, file=sio)
print(" value :", value, file=sio)
try:
ov = np.asarray(expected)
nv = np.asarray(value)
ssio = StringIO()
absdiff = np.absolute(nv - ov)
print(" Max Abs Diff: ", np.max(absdiff), file=ssio)
print(" Mean Abs Diff: ", np.mean(absdiff), file=ssio)
print(" Median Abs Diff: ", np.median(absdiff), file=ssio)
print(" Std Abs Diff: ", np.std(absdiff), file=ssio)
reldiff = np.absolute(nv - ov) / np.absolute(ov)
print(" Max Rel Diff: ", np.max(reldiff), file=ssio)
print(" Mean Rel Diff: ", np.mean(reldiff), file=ssio)
print(" Median Rel Diff: ", np.median(reldiff), file=ssio)
print(" Std Rel Diff: ", np.std(reldiff), file=ssio)
# only if all succeeds to we add anything to sio
print(ssio.getvalue(), file=sio)
except Exception:
pass
atol_, rtol_ = T.basic._get_atol_rtol(expected, value)
if rtol is not None:
rtol_ = rtol
if atol is not None:
atol_ = atol
print(" rtol, atol:", rtol_, atol_, file=sio)
return sio.getvalue()
def normalize_token_spacing(code):
tokens = [(t[0], t[1])
for t in tokenize.generate_tokens(StringIO(code).readline)]
return pretty_untokenize(tokens)
def __repr__(self):
file_obj = StringIO()
file_obj.write('<%s object> n=%s\n' % (self.type, self.n))
self.write_card(file_obj)
return file_obj.getvalue()
def test_dump_info():
cs = StringIO()
debug.dump_info(None, None, file=cs, testing=True)
assert cs.getvalue()
def mock_keyfile(*args, **kwargs):
yield StringIO('a' * 50)
def test_01_02_load_v2(self):
data = r"""CellProfiler Pipeline: http://www.cellprofiler.org
Version:1
SVNRevision:9524
LoadSingleImage:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
Folder containing the image file:Default Input Folder\x7CNone
Filename of the image to load (Include the extension, e.g., .tif):foo.tif
Name the image that will be loaded:DNA
Filename of the image to load (Include the extension, e.g., .tif):bar.tif
Name the image that will be loaded:Cytoplasm
LoadSingleImage:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
Folder containing the image file:Default Output Folder\x7CNone
Filename of the image to load (Include the extension, e.g., .tif):baz.tif
Name the image that will be loaded:GFP
LoadSingleImage:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
Folder containing the image file:Elsewhere...\x7CNone
Filename of the image to load (Include the extension, e.g., .tif):baz.tif
Name the image that will be loaded:GFP
LoadSingleImage:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:True|notes:\x5B\x5D]
Folder containing the image file:URL\x7Chttps\x3A//svn.broadinstitute.org/CellProfiler/trunk/ExampleImages/ExampleSBSImages
Filename of the image to load (Include the extension, e.g., .tif):Channel1-01-A-01.tif
Name the image that will be loaded:DNA1
"""
pipeline = cellprofiler.pipeline.Pipeline()
def callback(caller, event):
self.assertFalse(
isinstance(event, cellprofiler.pipeline.LoadExceptionEvent))
pipeline.add_listener(callback)
pipeline.load(StringIO(data))
self.assertEqual(len(pipeline.modules()), 4)
module = pipeline.modules()[0]
self.assertTrue(
isinstance(module,
cellprofiler.modules.loadsingleimage.LoadSingleImage))
self.assertEqual(len(module.file_settings), 2)
fs = module.file_settings[0]
self.assertEqual(fs.file_name, "foo.tif")
self.assertEqual(fs.image_name, "DNA")
fs = module.file_settings[1]
self.assertEqual(fs.file_name, "bar.tif")
self.assertEqual(fs.image_name, "Cytoplasm")
module = pipeline.modules()[3]
fs = module.file_settings[0]
self.assertEqual(
fs.file_name,
"https://svn.broadinstitute.org/CellProfiler/trunk/ExampleImages/"
"ExampleSBSImages/Channel1-01-A-01.tif")
dir_choice = [
cellprofiler.setting.DEFAULT_INPUT_FOLDER_NAME,
cellprofiler.setting.DEFAULT_OUTPUT_FOLDER_NAME,
cellprofiler.setting.ABSOLUTE_FOLDER_NAME,
cellprofiler.setting.URL_FOLDER_NAME
]
for i, module in enumerate(pipeline.modules()):
self.assertTrue(
isinstance(
module,
cellprofiler.modules.loadsingleimage.LoadSingleImage))
self.assertEqual(module.directory.dir_choice, dir_choice[i])
def test_01_01_load_v1(self):
data = r"""CellProfiler Pipeline: http://www.cellprofiler.org
Version:1
SVNRevision:9524
LoadSingleImage:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
Folder containing the image file:Default Input Folder
Name of the folder containing the image file:path1
Filename of the image to load (Include the extension, e.g., .tif):foo.tif
Name the image that will be loaded:DNA
Filename of the image to load (Include the extension, e.g., .tif):bar.tif
Name the image that will be loaded:Cytoplasm
LoadSingleImage:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
Folder containing the image file:Default Output Folder
Name of the folder containing the image file:path2
Filename of the image to load (Include the extension, e.g., .tif):baz.tif
Name the image that will be loaded:GFP
LoadSingleImage:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
Folder containing the image file:Custom folder
Name of the folder containing the image file:path3
Filename of the image to load (Include the extension, e.g., .tif):baz.tif
Name the image that will be loaded:GFP
LoadSingleImage:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D]
Folder containing the image file:Custom with metadata
Name of the folder containing the image file:path4
Filename of the image to load (Include the extension, e.g., .tif):baz.tif
Name the image that will be loaded:GFP
"""
pipeline = cellprofiler.pipeline.Pipeline()
def callback(caller, event):
self.assertFalse(
isinstance(event, cellprofiler.pipeline.LoadExceptionEvent))
pipeline.add_listener(callback)
pipeline.load(StringIO(data))
self.assertEqual(len(pipeline.modules()), 4)
dir_choice = [
cellprofiler.setting.DEFAULT_INPUT_FOLDER_NAME,
cellprofiler.setting.DEFAULT_OUTPUT_FOLDER_NAME,
cellprofiler.setting.ABSOLUTE_FOLDER_NAME,
cellprofiler.setting.ABSOLUTE_FOLDER_NAME
]
for i, module in enumerate(pipeline.modules()):
self.assertTrue(
isinstance(
module,
cellprofiler.modules.loadsingleimage.LoadSingleImage))
self.assertEqual(module.directory.dir_choice, dir_choice[i])
self.assertEqual(module.directory.custom_path, "path%d" % (i + 1))
module = pipeline.modules()[0]
self.assertTrue(
isinstance(module,
cellprofiler.modules.loadsingleimage.LoadSingleImage))
self.assertEqual(len(module.file_settings), 2)
fs = module.file_settings[0]
self.assertEqual(fs.file_name, "foo.tif")
self.assertEqual(fs.image_name, "DNA")
fs = module.file_settings[1]
self.assertEqual(fs.file_name, "bar.tif")
self.assertEqual(fs.image_name, "Cytoplasm")
def test_unchecked_etag(self):
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj(self.datafile, check_etag=False)
self.assertTrue('ETag: d41d8cd98f00b204e9800998ecf8427e (not checked)'
in out.getvalue())
def test_print_obj_metadata(self):
self.assertRaisesMessage(ValueError, 'Metadata is None',
print_obj_metadata, [])
def get_metadata(items):
md = dict(name='/AUTH_admin/c/dummy')
md['Content-Type'] = 'application/octet-stream'
md['X-Timestamp'] = 106.3
md.update(items)
return md
metadata = get_metadata({'X-Object-Meta-Mtime': '107.3'})
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj_metadata(metadata)
exp_out = '''Path: /AUTH_admin/c/dummy
Account: AUTH_admin
Container: c
Object: dummy
Object hash: 128fdf98bddd1b1e8695f4340e67a67a
Content-Type: application/octet-stream
Timestamp: 1970-01-01T00:01:46.300000 (%s)
System Metadata:
No metadata found
User Metadata:
X-Object-Meta-Mtime: 107.3
Other Metadata:
No metadata found''' % (utils.Timestamp(106.3).internal)
self.assertEqual(out.getvalue().strip(), exp_out)
metadata = get_metadata({
'X-Object-Sysmeta-Mtime': '107.3',
'X-Object-Sysmeta-Name': 'Obj name',
})
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj_metadata(metadata)
exp_out = '''Path: /AUTH_admin/c/dummy
Account: AUTH_admin
Container: c
Object: dummy
Object hash: 128fdf98bddd1b1e8695f4340e67a67a
Content-Type: application/octet-stream
Timestamp: 1970-01-01T00:01:46.300000 (%s)
System Metadata:
X-Object-Sysmeta-Mtime: 107.3
X-Object-Sysmeta-Name: Obj name
User Metadata:
No metadata found
Other Metadata:
No metadata found''' % (utils.Timestamp(106.3).internal)
self.assertEqual(out.getvalue().strip(), exp_out)
metadata = get_metadata({
'X-Object-Meta-Mtime': '107.3',
'X-Object-Sysmeta-Mtime': '107.3',
'X-Object-Mtime': '107.3',
})
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj_metadata(metadata)
exp_out = '''Path: /AUTH_admin/c/dummy
Account: AUTH_admin
Container: c
Object: dummy
Object hash: 128fdf98bddd1b1e8695f4340e67a67a
Content-Type: application/octet-stream
Timestamp: 1970-01-01T00:01:46.300000 (%s)
System Metadata:
X-Object-Sysmeta-Mtime: 107.3
User Metadata:
X-Object-Meta-Mtime: 107.3
Other Metadata:
X-Object-Mtime: 107.3''' % (utils.Timestamp(106.3).internal)
self.assertEqual(out.getvalue().strip(), exp_out)
metadata = get_metadata({})
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj_metadata(metadata)
exp_out = '''Path: /AUTH_admin/c/dummy
Account: AUTH_admin
Container: c
Object: dummy
Object hash: 128fdf98bddd1b1e8695f4340e67a67a
Content-Type: application/octet-stream
Timestamp: 1970-01-01T00:01:46.300000 (%s)
System Metadata:
No metadata found
User Metadata:
No metadata found
Other Metadata:
No metadata found''' % (utils.Timestamp(106.3).internal)
self.assertEqual(out.getvalue().strip(), exp_out)
metadata = get_metadata({'X-Object-Meta-Mtime': '107.3'})
metadata['name'] = '/a-s'
self.assertRaisesMessage(ValueError, 'Path is invalid',
print_obj_metadata, metadata)
metadata = get_metadata({'X-Object-Meta-Mtime': '107.3'})
del metadata['name']
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj_metadata(metadata)
exp_out = '''Path: Not found in metadata
Content-Type: application/octet-stream
Timestamp: 1970-01-01T00:01:46.300000 (%s)
System Metadata:
No metadata found
User Metadata:
X-Object-Meta-Mtime: 107.3
Other Metadata:
No metadata found''' % (utils.Timestamp(106.3).internal)
self.assertEqual(out.getvalue().strip(), exp_out)
metadata = get_metadata({'X-Object-Meta-Mtime': '107.3'})
del metadata['Content-Type']
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj_metadata(metadata)
exp_out = '''Path: /AUTH_admin/c/dummy
Account: AUTH_admin
Container: c
Object: dummy
Object hash: 128fdf98bddd1b1e8695f4340e67a67a
Content-Type: Not found in metadata
Timestamp: 1970-01-01T00:01:46.300000 (%s)
System Metadata:
No metadata found
User Metadata:
X-Object-Meta-Mtime: 107.3
Other Metadata:
No metadata found''' % (utils.Timestamp(106.3).internal)
self.assertEqual(out.getvalue().strip(), exp_out)
metadata = get_metadata({'X-Object-Meta-Mtime': '107.3'})
del metadata['X-Timestamp']
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj_metadata(metadata)
exp_out = '''Path: /AUTH_admin/c/dummy
Account: AUTH_admin
Container: c
Object: dummy
Object hash: 128fdf98bddd1b1e8695f4340e67a67a
Content-Type: application/octet-stream
Timestamp: Not found in metadata
System Metadata:
No metadata found
User Metadata:
X-Object-Meta-Mtime: 107.3
Other Metadata:
No metadata found'''
self.assertEqual(out.getvalue().strip(), exp_out)
def test_print_obj_policy_name_mismatch(self):
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj(self.datafile, policy_name='two', swift_dir=self.testdir)
ring_alert_msg = 'Warning: Ring does not match policy!'
self.assertTrue(ring_alert_msg in out.getvalue())
def test_print_obj(self):
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj(self.datafile, swift_dir=self.testdir)
self.assertTrue('/objects-1/' in out.getvalue())
def test_missing_etag(self):
out = StringIO()
with mock.patch('sys.stdout', out):
print_obj(self.datafile)
self.assertTrue('ETag: Not found in metadata' in out.getvalue())
def getEmptyFileStoreID(self, jobStoreID=None):
fileID = self._newID(isFile=True, jobStoreID=jobStoreID)
self._writeFile(fileID, StringIO(""))
return fileID
def try_den_weight_torsion(self, grid_pair):
#backup_k_rep = self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep
local_seed = int(self.random_seed + grid_pair[1])
flex.set_random_seed(value=local_seed)
random.seed(local_seed)
self.fmodels.fmodel_xray().xray_structure.replace_scatterers(
self.save_scatterers_local.deep_copy())
self.fmodels.update_xray_structure(
xray_structure=self.fmodels.fmodel_xray().xray_structure,
update_f_calc=True)
utils.assert_xray_structures_equal(
x1=self.fmodels.fmodel_xray().xray_structure,
x2=self.model.get_xray_structure())
gamma_local = grid_pair[0]
weight_local = grid_pair[1]
self.model.restraints_manager.geometry.\
den_manager.gamma = gamma_local
self.model.restraints_manager.geometry.\
den_manager.weight = weight_local
cycle = 0
self.model.restraints_manager.geometry.\
den_manager.current_cycle = cycle+1
num_den_cycles = self.model.restraints_manager.geometry.\
den_manager.num_cycles
if self.params.den.optimize and \
self.nproc != Auto and \
self.nproc > 1:
local_log = sys.stdout
elif self.params.den.optimize and \
self.nproc == 1:
if self.verbose:
local_log = self.log
else:
local_log = StringIO()
else:
local_log = self.log
print(" ...trying gamma %.1f, weight %.1f" %
(gamma_local, weight_local),
file=self.log)
while cycle < num_den_cycles:
#if self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.current_cycle == \
# self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.torsion_mid_point+1:
# self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep = 1.0
print("DEN cycle %d" % (cycle + 1), file=local_log)
#print >> local_log, "Random seed: %d" % flex.get_random_seed()
r_free = self.fmodels.fmodel_xray().r_free()
print("rfree at start of SA cycle: %.4f" % r_free, file=local_log)
print("k_rep = %.2f" % \
self.params.tardy.\
prolsq_repulsion_function_changes.k_rep, file=local_log)
tardy.run(fmodels=self.fmodels,
model=self.model,
target_weights=self.target_weights,
params=self.params.tardy,
log=local_log,
format_for_phenix_refine=True,
call_back_after_step=False)
if self.params.den.bulk_solvent_and_scale:
self.bulk_solvent_and_scale(log=local_log)
self.fmodels.fmodel_xray(
).xray_structure = self.model.get_xray_structure()
if self.params.den.refine_adp:
self.adp_refinement(log=local_log)
self.model.torsion_ncs_restraints_update(log=local_log)
cycle += 1
self.model.restraints_manager.geometry.\
den_manager.current_cycle += 1
r_free = self.fmodels.fmodel_xray().r_free()
print("rfree at end of SA cycle: %f" % r_free, file=local_log)
r_free = self.fmodels.fmodel_xray().r_free()
step_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
step_eq_distances = self.model.restraints_manager.geometry.\
den_manager.get_current_eq_distances()
return (gamma_local, weight_local, r_free, step_xray_structure,
step_eq_distances)
def _writeString(self, jobStoreID, stringToUpload, **kwarg):
self._writeFile(jobStoreID, StringIO(stringToUpload), **kwarg)
def try_den_weight_cartesian(self, grid_pair):
local_seed = int(self.random_seed + grid_pair[1])
flex.set_random_seed(value=local_seed)
random.seed(local_seed)
self.fmodels.fmodel_xray().xray_structure.replace_scatterers(
self.save_scatterers_local.deep_copy())
self.fmodels.update_xray_structure(
xray_structure=self.fmodels.fmodel_xray().xray_structure,
update_f_calc=True)
utils.assert_xray_structures_equal(
x1=self.fmodels.fmodel_xray().xray_structure,
x2=self.model.get_xray_structure())
gamma_local = grid_pair[0]
weight_local = grid_pair[1]
self.model.restraints_manager.geometry.\
den_manager.gamma = gamma_local
self.model.restraints_manager.geometry.\
den_manager.weight = weight_local
cycle = 0
self.model.restraints_manager.geometry.\
den_manager.current_cycle = cycle+1
num_den_cycles = self.model.restraints_manager.geometry.\
den_manager.num_cycles
if self.params.den.optimize and \
self.nproc != Auto and \
self.nproc > 1:
local_log = sys.stdout
elif self.params.den.optimize and \
self.nproc == 1:
if self.verbose:
local_log = self.log
else:
local_log = StringIO()
else:
local_log = self.log
print(" ...trying gamma %f, weight %f" % (gamma_local, weight_local),
file=self.log)
while cycle < num_den_cycles:
print("DEN cycle %s" % (cycle + 1), file=local_log)
r_free = self.fmodels.fmodel_xray().r_free()
print("rfree at start of SA cycle: %f" % r_free, file=local_log)
simulated_annealing.manager(params=self.params.simulated_annealing,
target_weights=self.target_weights,
macro_cycle=self.macro_cycle,
h_params=self.params.hydrogens,
fmodels=self.fmodels,
model=self.model,
all_params=self.params,
out=local_log)
if self.params.den.bulk_solvent_and_scale:
self.bulk_solvent_and_scale(log=local_log)
if self.params.den.refine_adp:
self.adp_refinement(log=local_log)
self.model.torsion_ncs_restraints_update(log=local_log)
cycle += 1
self.model.restraints_manager.geometry.\
den_manager.current_cycle += 1
r_free = self.fmodels.fmodel_xray().r_free()
print("rfree at end of SA cycle: %f" % r_free, file=local_log)
r_free = self.fmodels.fmodel_xray().r_free()
step_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
step_eq_distances = self.model.restraints_manager.geometry.\
den_manager.get_current_eq_distances()
return (gamma_local, weight_local, r_free, step_xray_structure,
step_eq_distances)
def exercise_combine_unique_pdb_files():
for file_name, s in [("tmp1", "1"), ("tmp2", " 2"), ("tmp3", "1\t"),
("tmp4", " \t2"), ("tmp5", "1 ")]:
open(file_name, "w").write(s)
for file_names in [[], ["tmp1"], ["tmp1", "tmp2"]]:
c = pdb.combine_unique_pdb_files(file_names=file_names)
assert len(c.file_name_registry) == len(file_names)
assert len(c.md5_registry) == len(file_names)
assert len(c.unique_file_names) == len(file_names)
assert len(c.raw_records) == len(file_names)
s = StringIO()
c.report_non_unique(out=s)
assert len(s.getvalue()) == 0
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp1"])
assert len(c.file_name_registry) == 1
assert len(c.md5_registry) == 1
assert len(c.unique_file_names) == 1
assert len(c.raw_records) == 1
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(
s.getvalue(), """\
INFO: PDB file name appears 2 times: "tmp1"
1 repeated file name ignored.
""")
c = pdb.combine_unique_pdb_files(
file_names=["tmp1", "tmp1", "tmp2", "tmp1"])
assert len(c.file_name_registry) == 2
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s, prefix="^")
assert not show_diff(
s.getvalue(), """\
^INFO: PDB file name appears 3 times: "tmp1"
^ 2 repeated file names ignored.
^
""")
c = pdb.combine_unique_pdb_files(file_names=["tmp1", "tmp2", "tmp3"])
assert len(c.file_name_registry) == 3
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(
s.getvalue(), """\
INFO: PDB files with identical content:
"tmp1"
"tmp3"
1 file with repeated content ignored.
""")
c = pdb.combine_unique_pdb_files(
file_names=["tmp1", "tmp2", "tmp3", "tmp5"])
assert len(c.file_name_registry) == 4
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s, prefix=": ")
assert not show_diff(
s.getvalue(), """\
: INFO: PDB files with identical content:
: "tmp1"
: "tmp3"
: "tmp5"
: 2 files with repeated content ignored.
:
""")
c = pdb.combine_unique_pdb_files(
file_names=["tmp1", "tmp2", "tmp3", "tmp4", "tmp5", "tmp4", "tmp5"])
assert len(c.file_name_registry) == 5
assert len(c.md5_registry) == 2
assert len(c.unique_file_names) == 2
assert len(c.raw_records) == 2
s = StringIO()
c.report_non_unique(out=s)
assert not show_diff(
s.getvalue(), """\
INFO: PDB file name appears 2 times: "tmp4"
INFO: PDB file name appears 2 times: "tmp5"
2 repeated file names ignored.
INFO: PDB files with identical content:
"tmp2"
"tmp4"
INFO: PDB files with identical content:
"tmp1"
"tmp3"
"tmp5"
3 files with repeated content ignored.
""")
def __init__(self, path):
self._output = StringIO()
self._path = path
def test_write_values_disconnects():
s = StringIO()
tst = "foo" * 100
writer.write_values(s, [tst], [(0, "disconnect")], blocksize=5)
assert not s.getvalue()
def test_debugprint():
A = tensor.matrix(name='A')
B = tensor.matrix(name='B')
C = A + B
C.name = 'C'
D = tensor.matrix(name='D')
E = tensor.matrix(name='E')
F = D + E
G = C + F
mode = theano.compile.get_default_mode().including('fusion')
g = theano.function([A, B, D, E], G, mode=mode)
# just test that it work
s = StringIO()
debugprint(G, file=s)
# test ids=int
s = StringIO()
debugprint(G, file=s, ids='int')
s = s.getvalue()
# The additional white space are needed!
reference = '\n'.join([
"Elemwise{add,no_inplace} [id 0] '' ",
" |Elemwise{add,no_inplace} [id 1] 'C' ",
" | |A [id 2]",
" | |B [id 3]",
" |Elemwise{add,no_inplace} [id 4] '' ",
" |D [id 5]",
" |E [id 6]",
]) + '\n'
if s != reference:
print('--' + s + '--')
print('--' + reference + '--')
assert s == reference
# test ids=CHAR
s = StringIO()
debugprint(G, file=s, ids='CHAR')
s = s.getvalue()
# The additional white space are needed!
reference = "\n".join([
"Elemwise{add,no_inplace} [id A] '' ",
" |Elemwise{add,no_inplace} [id B] 'C' ",
" | |A [id C]",
" | |B [id D]",
" |Elemwise{add,no_inplace} [id E] '' ",
" |D [id F]",
" |E [id G]",
]) + '\n'
if s != reference:
print('--' + s + '--')
print('--' + reference + '--')
assert s == reference
# test ids=CHAR, stop_on_name=True
s = StringIO()
debugprint(G, file=s, ids='CHAR', stop_on_name=True)
s = s.getvalue()
# The additional white space are needed!
reference = '\n'.join([
"Elemwise{add,no_inplace} [id A] '' ",
" |Elemwise{add,no_inplace} [id B] 'C' ",
" |Elemwise{add,no_inplace} [id C] '' ",
" |D [id D]",
" |E [id E]",
]) + '\n'
if s != reference:
print('--' + s + '--')
print('--' + reference + '--')
assert s == reference
# test ids=
s = StringIO()
debugprint(G, file=s, ids='')
s = s.getvalue()
# The additional white space are needed!
reference = '\n'.join([
"Elemwise{add,no_inplace} '' ",
" |Elemwise{add,no_inplace} 'C' ",
" | |A ",
" | |B ",
" |Elemwise{add,no_inplace} '' ",
" |D ",
" |E ",
]) + '\n'
if s != reference:
print('--' + s + '--')
print('--' + reference + '--')
assert s == reference
# test print_storage=True
s = StringIO()
debugprint(g, file=s, ids='', print_storage=True)
s = s.getvalue()
# The additional white space are needed!
reference = '\n'.join([
"Elemwise{add,no_inplace} '' 0 [None]",
" |A [None]",
" |B [None]",
" |D [None]",
" |E [None]",
]) + '\n'
if s != reference:
print('--' + s + '--')
print('--' + reference + '--')
assert s == reference
# test clients
s = StringIO()
# We must force the mode as otherwise it can change the clients order
f = theano.function([A, B, D], [A + B, A + B - D], mode='FAST_COMPILE')
debugprint(f, file=s, print_clients=True)
s = s.getvalue()
# The additional white space are needed!
reference = '\n'.join([
"Elemwise{add,no_inplace} [id A] '' 0 clients:[('[id B]', 1), ('output', '')]",
" |A [id D]",
" |B [id E]",
"Elemwise{sub,no_inplace} [id B] '' 1",
" |Elemwise{add,no_inplace} [id A] '' 0 clients:[('[id B]', 1), ('output', '')]",
" |D [id F]",
]) + '\n'
if s != reference:
print('--' + s + '--')
print('--' + reference + '--')
assert s == reference
def c_code(self, node, name, inputs, outputs, sub):
inp_ndim = node.inputs[0].ndim
inp = inputs[0]
indices = inputs[1:]
# pad out the index list to the same dimension as the input
idx_list = self.idx_list + \
((slice(None),) * (inp_ndim - len(self.idx_list)))
# This case fails when we use pygpu_index(), so here is some
# special code
if len(idx_list) == 0:
return """
Py_XDECREF(%(out)s);
%(out)s = pygpu_copy(%(inp)s, GA_ANY_ORDER);
if (!%(out)s) {
// Exception already set
%(fail)s
}
""" % dict(out=outputs[0], inp=inp, fail=sub['fail'])
sio = StringIO()
print("""
ssize_t starts[%(sz)s];
ssize_t stops[%(sz)s];
ssize_t steps[%(sz)s];
ssize_t cur;
int err;
if (%(inp)s->ga.nd != %(sz)s) {
PyErr_SetString(PyExc_IndexError, "invalid index");
%(fail)s
}
""" % dict(sz=len(idx_list), inp=inp, fail=sub['fail']), file=sio)
def fix_idx(idx):
if idx is None:
return "0", 1
elif isinstance(idx, (np.integer, integer_types)):
return str(idx), 0
elif isinstance(idx, gof.Type):
return indices.pop(0), 0
else:
assert 0, idx
for i, idx in enumerate(idx_list):
if isinstance(idx, slice):
start, start_n = fix_idx(idx.start)
stop, stop_n = fix_idx(idx.stop)
step, step_n = fix_idx(idx.step)
print("""
starts[%(i)s] = %(start)s;
stops[%(i)s] = %(stop)s;
steps[%(i)s] = %(step)s;
if (fix_indices(&starts[%(i)s], &stops[%(i)s], &steps[%(i)s],
%(start_n)s, %(stop_n)s, %(step_n)s,
%(inp)s->ga.dimensions[%(i)s]) == -1) {
%(fail)s
}
""" % dict(i=i, start=start, stop=stop, step=step,
start_n=start_n, stop_n=stop_n, step_n=step_n,
fail=sub['fail'], inp=inp), file=sio)
else:
if isinstance(idx, gof.Type):
start = indices.pop(0)
elif isinstance(idx, (np.integer, integer_types)):
start = idx
else:
assert 0, idx
print("""
cur = %(start)s;
if (cur < 0)
cur += %(inp)s->ga.dimensions[%(i)s];
starts[%(i)s] = cur;
steps[%(i)s] = 0;
""" % dict(i=i, start=start, fail=sub['fail'], inp=inp), file=sio)
print("""
Py_XDECREF(%(out)s);
%(out)s = pygpu_index(%(inp)s, starts, stops, steps);
if (!%(out)s) { %(fail)s }
""" % dict(name=name, fail=sub['fail'], inp=inp, out=outputs[0]), file=sio)
return sio.getvalue()
def exercise_simple():
pdb_str = """
ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N
ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C
ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C
ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O
ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C
ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C
ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C
ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C
ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C
ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C
ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C
ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O
ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O
TER
"""
pdb_in = iotbx.pdb.input(source_info=None, lines=pdb_str)
hierarchy = pdb_in.construct_hierarchy()
xrs = pdb_in.xray_structure_simple()
xrs.scattering_type_registry(d_min=1.5, table="n_gaussian")
xrs.set_inelastic_form_factors(photon=1.54, table="sasaki")
file_base = "tmp_mmtbx_cmdline"
with open(file_base + ".pdb", "w") as f:
f.write(hierarchy.as_pdb_string(crystal_symmetry=xrs))
fc = abs(xrs.structure_factors(d_min=1.5).f_calc())
flags = fc.generate_r_free_flags()
mtz = fc.as_mtz_dataset(column_root_label="F")
mtz.add_miller_array(flags, column_root_label="FreeR_flag")
mtz.mtz_object().write(file_base + ".mtz")
with open(file_base + ".fa", "w") as f:
f.write(">Tyr\nY\n")
base_args = [file_base + ext for ext in [".pdb", ".mtz", ".fa"]]
cmdline = mmtbx.command_line.load_model_and_data(
args=base_args + ["wavelength=1.54"],
master_phil=mmtbx.command_line.generate_master_phil_with_inputs(""),
out=StringIO(),
create_log_buffer=True)
assert (cmdline.params.input.xray_data.file_name is not None)
assert (cmdline.sequence is not None)
r_factor = cmdline.fmodel.r_work()
assert (r_factor < 0.002)
cmdline.save_data_mtz("tmp_mmtbx_cmdline_data.mtz")
assert os.path.isfile("tmp_mmtbx_cmdline_data.mtz")
model = cmdline.create_model_manager()
# energy input
cmdline = mmtbx.command_line.load_model_and_data(
args=base_args + ["energy=8050"],
master_phil=mmtbx.command_line.generate_master_phil_with_inputs(""),
out=StringIO(),
create_log_buffer=True)
assert approx_equal(cmdline.params.input.wavelength, 1.54018, eps=0.0001)
# UNMERGED DATA INPUT
log = cmdline.start_log_file("tst_mmtbx_cmdline.log")
fc2 = xrs.structure_factors(d_min=1.3).f_calc().generate_bijvoet_mates()
fc2 = fc2.randomize_amplitude_and_phase(
amplitude_error=0.01, phase_error_deg=5,
random_seed=12345).customized_copy(
sigmas=flex.random_double(fc2.size(), 10))
i_obs = abs(fc2).f_as_f_sq()
i_obs = i_obs.expand_to_p1().customized_copy(
crystal_symmetry=fc2).set_observation_type_xray_intensity()
with open(file_base + ".sca", "w") as f:
no_merge_original_index.writer(i_obs, file_object=f)
master_phil = mmtbx.command_line.generate_master_phil_with_inputs(
phil_string="", enable_unmerged_data=True)
cmdline = mmtbx.command_line.load_model_and_data(
args=[file_base + ext for ext in [
".pdb",
".mtz",
".fa",
]] + ["unmerged_data.file_name=%s.sca" % file_base],
master_phil=master_phil,
out=StringIO(),
create_log_buffer=True)
assert (cmdline.unmerged_i_obs is not None)
# test with unknown scatterers
pdb_in = iotbx.pdb.input(source_info=None,
lines=pdb_str + """\
ATOM 59 UNK UNL A 7 0.000 0.000 0.000 1.00 20.00 X
""")
hierarchy = pdb_in.construct_hierarchy()
file_base = "tmp_mmtbx_cmdline"
with open(file_base + ".pdb", "w") as f:
f.write(hierarchy.as_pdb_string(crystal_symmetry=xrs))
try:
cmdline = mmtbx.command_line.load_model_and_data(
args=[file_base + ext for ext in [
".pdb",
".mtz",
".fa",
]],
master_phil=master_phil,
out=StringIO(),
process_pdb_file=False,
create_log_buffer=True)
except Sorry:
pass
else:
raise Exception_expected
cmdline = mmtbx.command_line.load_model_and_data(
args=[file_base + ext for ext in [
".pdb",
".mtz",
".fa",
]],
master_phil=master_phil,
out=StringIO(),
process_pdb_file=False,
create_log_buffer=True,
remove_unknown_scatterers=True)
def tokenize_str(code):
return list(tokenize.generate_tokens(StringIO(code).readline))
def exercise_load_unmerged():
flex.set_random_seed(123456)
random.seed(123456)
base = "tst_load_unmerged"
pdb_in = iotbx.pdb.hierarchy.input(pdb_string=model_1yjp)
xrs = pdb_in.xray_structure_simple()
xrs.set_inelastic_form_factors(photon=1.54, table="sasaki")
fc = abs(xrs.structure_factors(d_min=1.5).f_calc()).average_bijvoet_mates()
fc.set_observation_type_xray_amplitude()
flags = fc.generate_r_free_flags()
mtz = fc.as_mtz_dataset(column_root_label="F")
mtz.add_miller_array(flags, column_root_label="FreeR_flag")
mtz.mtz_object().write(base + ".mtz")
xrs_p1 = xrs.expand_to_p1()
xrs_p1.shake_sites_in_place(rms_difference=0.1)
fc_p1 = xrs_p1.structure_factors(d_min=1.4).f_calc()
fc_p1_extra = fc_p1.randomize_amplitude_and_phase(amplitude_error=1.0,
phase_error_deg=0,
random_seed=123456)
fc_p1 = abs(
fc_p1.concatenate(other=fc_p1_extra)).sort(by_value="packed_indices")
fc_p1.set_observation_type_xray_amplitude()
sg_p2 = sgtbx.space_group_info("P2")
ic = fc_p1.f_as_f_sq().customized_copy(space_group_info=sg_p2,
sigmas=flex.double(
fc_p1.size(), 10.0))
ic.export_as_scalepack_unmerged(file_name=base + ".sca")
open(base + ".pdb", "w").write(model_1yjp)
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s.sca" % base,
]
master_phil = mmtbx.command_line.generate_master_phil_with_inputs(
phil_string="", enable_unmerged_data=True)
cmdline = mmtbx.command_line.load_model_and_data(
args=[base + ext for ext in [
".pdb",
".mtz",
]] + ["unmerged_data.file_name=%s.sca" % base],
master_phil=master_phil,
out=StringIO(),
create_fmodel=False,
process_pdb_file=False,
create_log_buffer=True)
# now with .sca in P1 (raises Sorry)
ic2 = fc_p1.f_as_f_sq().customized_copy(
sigmas=flex.double(fc_p1.size(), 10.0))
ic2.export_as_scalepack_unmerged(file_name=base + "_p1.sca")
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s_p1.sca" % base,
]
try:
cmdline = mmtbx.command_line.load_model_and_data(
args=[base + ext for ext in [
".pdb",
".mtz",
]] + ["unmerged_data.file_name=%s_p1.sca" % base],
master_phil=master_phil,
out=StringIO(),
create_fmodel=False,
process_pdb_file=False,
create_log_buffer=True)
except Sorry as s:
assert (
str(s) ==
"Incompatible space groups in merged and unmerged data:P 1 21 1 versus P 1"
), s
else:
raise Exception_expected
# XXX
f = open(base + ".cif", "w")
ic.as_cif_simple(array_type="meas", out=f)
f.close()
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s.cif" % base,
]
cmdline = mmtbx.command_line.load_model_and_data(
args=[base + ext for ext in [
".pdb",
".mtz",
]] + ["unmerged_data.file_name=%s.cif" % base],
master_phil=master_phil,
out=StringIO(),
create_fmodel=False,
process_pdb_file=False,
create_log_buffer=True)
# bad unit cell
uc2 = uctbx.unit_cell((23, 6.5, 23.5, 90, 108, 90))
ic3 = ic.customized_copy(unit_cell=uc2)
f = open(base + "_new_uc.cif", "w")
ic3.as_cif_simple(array_type="meas", out=f)
f.close()
args = [
base + ".mtz",
base + ".pdb",
"unmerged_data=%s_new_uc.cif" % base,
]
try:
cmdline = mmtbx.command_line.load_model_and_data(
args=[base + ext for ext in [
".pdb",
".mtz",
]] + ["unmerged_data.file_name=%s_new_uc.cif" % base],
master_phil=master_phil,
out=StringIO(),
create_fmodel=False,
process_pdb_file=False,
create_log_buffer=True)
except Sorry as s:
assert ("Incompatible symmetry definitions" in str(s)), s
else:
raise Exception_expected
def generate_ssl_cert(target_file=None,
overwrite=False,
random=False,
return_content=False,
serial_number=None):
# Note: Do NOT import "OpenSSL" at the root scope
# (Our test Lambdas are importing this file but don't have the module installed)
from OpenSSL import crypto
def all_exist(*files):
return all([os.path.exists(f) for f in files])
if target_file and not overwrite and os.path.exists(target_file):
key_file_name = '%s.key' % target_file
cert_file_name = '%s.crt' % target_file
try:
# extract key and cert from target_file and store into separate files
content = load_file(target_file)
key_start = '-----BEGIN PRIVATE KEY-----'
key_end = '-----END PRIVATE KEY-----'
cert_start = '-----BEGIN CERTIFICATE-----'
cert_end = '-----END CERTIFICATE-----'
key_content = content[content.index(key_start
):content.index(key_end) +
len(key_end)]
cert_content = content[content.index(cert_start
):content.index(cert_end) +
len(cert_end)]
save_file(key_file_name, key_content)
save_file(cert_file_name, cert_content)
except Exception as e:
LOG.info(
'Unable to store key/cert files for custom SSL certificate: %s'
% e)
if all_exist(key_file_name, cert_file_name):
return target_file, cert_file_name, key_file_name
if random and target_file:
if '.' in target_file:
target_file = target_file.replace('.', '.%s.' % short_uid(), 1)
else:
target_file = '%s.%s' % (target_file, short_uid())
# create a key pair
k = crypto.PKey()
k.generate_key(crypto.TYPE_RSA, 2048)
# create a self-signed cert
cert = crypto.X509()
subj = cert.get_subject()
subj.C = 'AU'
subj.ST = 'Some-State'
subj.L = 'Some-Locality'
subj.O = 'LocalStack Org' # noqa
subj.OU = 'Testing'
subj.CN = 'localhost'
# Note: new requirements for recent OSX versions: https://support.apple.com/en-us/HT210176
# More details: https://www.iol.unh.edu/blog/2019/10/10/macos-catalina-and-chrome-trust
serial_number = serial_number or 1001
cert.set_version(2)
cert.set_serial_number(serial_number)
cert.gmtime_adj_notBefore(0)
cert.gmtime_adj_notAfter(2 * 365 * 24 * 60 * 60)
cert.set_issuer(cert.get_subject())
cert.set_pubkey(k)
alt_names = b'DNS:localhost,DNS:test.localhost.atlassian.io,IP:127.0.0.1'
cert.add_extensions([
crypto.X509Extension(b'subjectAltName', False, alt_names),
crypto.X509Extension(b'basicConstraints', True, b'CA:false'),
crypto.X509Extension(
b'keyUsage', True,
b'nonRepudiation,digitalSignature,keyEncipherment'),
crypto.X509Extension(b'extendedKeyUsage', True, b'serverAuth')
])
cert.sign(k, 'SHA256')
cert_file = StringIO()
key_file = StringIO()
cert_file.write(to_str(crypto.dump_certificate(crypto.FILETYPE_PEM, cert)))
key_file.write(to_str(crypto.dump_privatekey(crypto.FILETYPE_PEM, k)))
cert_file_content = cert_file.getvalue().strip()
key_file_content = key_file.getvalue().strip()
file_content = '%s\n%s' % (key_file_content, cert_file_content)
if target_file:
key_file_name = '%s.key' % target_file
cert_file_name = '%s.crt' % target_file
# check existence to avoid permission denied issues:
# https://github.com/localstack/localstack/issues/1607
if not all_exist(target_file, key_file_name, cert_file_name):
for i in range(2):
try:
save_file(target_file, file_content)
save_file(key_file_name, key_file_content)
save_file(cert_file_name, cert_file_content)
break
except Exception as e:
if i > 0:
raise
LOG.info(
'Unable to store certificate file under %s, using tmp file instead: %s'
% (target_file, e))
# Fix for https://github.com/localstack/localstack/issues/1743
target_file = '%s.pem' % new_tmp_file()
key_file_name = '%s.key' % target_file
cert_file_name = '%s.crt' % target_file
TMP_FILES.append(target_file)
TMP_FILES.append(key_file_name)
TMP_FILES.append(cert_file_name)
if not return_content:
return target_file, cert_file_name, key_file_name
return file_content
def setup(self):
from six.moves import cStringIO as StringIO
self.packet, self.socket = self.request
self.rfile = StringIO(self.packet)
self.wfile = StringIO(self.packet)
def __init__(self):
self._out = StringIO()
self.indentation = 0
def test_print_db_info_metadata(self):
self.assertRaisesMessage(ValueError, 'Wrong DB type',
print_db_info_metadata, 't', {}, {})
self.assertRaisesMessage(ValueError, 'DB info is None',
print_db_info_metadata, 'container', None, {})
self.assertRaisesMessage(ValueError, 'Info is incomplete',
print_db_info_metadata, 'container', {}, {})
info = dict(account='acct',
created_at=100.1,
put_timestamp=106.3,
delete_timestamp=107.9,
status_changed_at=108.3,
container_count='3',
object_count='20',
bytes_used='42')
info['hash'] = 'abaddeadbeefcafe'
info['id'] = 'abadf100d0ddba11'
md = {
'x-account-meta-mydata': ('swift', '0000000000.00000'),
'x-other-something': ('boo', '0000000000.00000')
}
out = StringIO()
with mock.patch('sys.stdout', out):
print_db_info_metadata('account', info, md)
exp_out = '''Path: /acct
Account: acct
Account Hash: dc5be2aa4347a22a0fee6bc7de505b47
Metadata:
Created at: 1970-01-01T00:01:40.100000 (100.1)
Put Timestamp: 1970-01-01T00:01:46.300000 (106.3)
Delete Timestamp: 1970-01-01T00:01:47.900000 (107.9)
Status Timestamp: 1970-01-01T00:01:48.300000 (108.3)
Container Count: 3
Object Count: 20
Bytes Used: 42
Chexor: abaddeadbeefcafe
UUID: abadf100d0ddba11
X-Other-Something: boo
No system metadata found in db file
User Metadata: {'mydata': 'swift'}'''
self.assertEqual(sorted(out.getvalue().strip().split('\n')),
sorted(exp_out.split('\n')))
info = dict(account='acct',
container='cont',
storage_policy_index=0,
created_at='0000000100.10000',
put_timestamp='0000000106.30000',
delete_timestamp='0000000107.90000',
status_changed_at='0000000108.30000',
object_count='20',
bytes_used='42',
reported_put_timestamp='0000010106.30000',
reported_delete_timestamp='0000010107.90000',
reported_object_count='20',
reported_bytes_used='42',
x_container_foo='bar',
x_container_bar='goo')
info['hash'] = 'abaddeadbeefcafe'
info['id'] = 'abadf100d0ddba11'
md = {'x-container-sysmeta-mydata': ('swift', '0000000000.00000')}
out = StringIO()
with mock.patch('sys.stdout', out):
print_db_info_metadata('container', info, md)
exp_out = '''Path: /acct/cont
Account: acct
Container: cont
Container Hash: d49d0ecbb53be1fcc49624f2f7c7ccae
Metadata:
Created at: 1970-01-01T00:01:40.100000 (0000000100.10000)
Put Timestamp: 1970-01-01T00:01:46.300000 (0000000106.30000)
Delete Timestamp: 1970-01-01T00:01:47.900000 (0000000107.90000)
Status Timestamp: 1970-01-01T00:01:48.300000 (0000000108.30000)
Object Count: 20
Bytes Used: 42
Storage Policy: %s (0)
Reported Put Timestamp: 1970-01-01T02:48:26.300000 (0000010106.30000)
Reported Delete Timestamp: 1970-01-01T02:48:27.900000 (0000010107.90000)
Reported Object Count: 20
Reported Bytes Used: 42
Chexor: abaddeadbeefcafe
UUID: abadf100d0ddba11
X-Container-Bar: goo
X-Container-Foo: bar
System Metadata: {'mydata': 'swift'}
No user metadata found in db file''' % POLICIES[0].name
self.assertEqual(sorted(out.getvalue().strip().split('\n')),
sorted(exp_out.split('\n')))
