def set_experiment_resource(remote: BossRemote, params: dict) -> ExperimentResource:
"""Use the arguments in the class config to create an experiment resource object"""
if 'name' not in params:
params['name'] = 'experiment{0}'.format(hex(round(time.time()))[2:])
param_names = [str(p.name) for p in inspect.signature(ExperimentResource).parameters.values()]
filtered_params = {k: v for k, v in list(params.items()) if k in param_names} # Filter unexpected arguments
exp_resource = ExperimentResource(**filtered_params)
if exp_resource.name in remote.list_experiments(exp_resource.coll_name):
experiment = remote.update_project(exp_resource.name, exp_resource)
print('Updated experiment {0}'.format(exp_resource.name))
else:
experiment = remote.create_project(exp_resource)
print('Created experiment {0}'.format(exp_resource.name))
return experiment
def delete_collection(remote: BossRemote, collection):
coll_obj = None
coll_name = None
if isinstance(collection, CollectionResource):
coll_obj = collection
coll_name = collection.name
elif isinstance(collection, str):
coll_name = collection
coll_obj = remote.get_project(CollectionResource(name=coll_name))
if coll_name is not None:
print('Deleting experiments of collection "{0}"...'.format(coll_name))
exp_names = remote.list_experiments(coll_name)
for n in exp_names:
delete_experiment(remote, n, coll_name)
if coll_obj is not None:
print('Deleting collection "{0}"...'.format(coll_name))
remote.delete_project(coll_obj)
class TestRemoteListMethods(unittest.TestCase):
def setUp(self):
config = {
"protocol": "https",
"host": "test.theboss.io",
"token": "my_secret"
}
self.remote = BossRemote(config)
def test_list_collections(self):
with patch.object(Remote, 'list_project') as list_prj_fake:
list_prj_fake.return_value = []
actual = self.remote.list_collections()
self.assertEqual([], actual)
def test_list_experiments(self):
with patch.object(Remote, 'list_project') as list_prj_fake:
list_prj_fake.return_value = []
actual = self.remote.list_experiments('collection_alpha')
self.assertEqual([], actual)
def test_list_channels(self):
with patch.object(Remote, 'list_project') as list_prj_fake:
list_prj_fake.return_value = []
actual = self.remote.list_channels('collection_alpha',
'experiment_beta')
self.assertEqual([], actual)
def test_list_coordinate_frames(self):
with patch.object(Remote, 'list_project') as list_prj_fake:
list_prj_fake.return_value = []
actual = self.remote.list_coordinate_frames()
self.assertEqual([], actual)
class bossHandler:
"""
This is a class for interacting with BOSS. It basically is a wrapper for Intern.
"""
def __init__(self, collection_name):
"""
Constructor:
Takes the following argument:
:param collection_name: name of the collection in BOSS
:type collection_name: string
"""
self.collection_name = collection_name
try:
self.rmt = BossRemote()
except:
print('Unexpected Error:', sys.exc_info()[0])
# def get_collection_list(self):
# return self.rmt.list_collections()
def list_experiments(self):
"""
:return: all the experiments available in current collection
"""
exp_list = self.rmt.list_experiments(self.collection_name)
return exp_list
def select_experiment(self, experiment_name):
"""
Select an experiment to be added to this handler
"""
tmp = ExperimentResource(collection_name=self.collection_name,
name=experiment_name)
exp = self.rmt.get_project(tmp)
self.experiment = exp
# return exp
def get_experiment(self):
"""
:return: the currently selected experiment for this handler
"""
if hasattr(self, 'experiment'):
return self.experiment
else:
raise AttributeError(
'No experiment exists. First, select an experiment using select_experiment'
)
def list_channels(self):
"""
:return: all channel in currently selected experiment
"""
return self.rmt.list_channels(self.collection_name,
self.experiment.name)
def select_channel(self, channel_name):
"""
Select a channel to be added to this handler
"""
self.channel = self.rmt.get_channel(chan_name=channel_name,
coll_name=self.collection_name,
exp_name=self.experiment.name)
def get_coordinate_frame(self):
"""
Return: current experiment's coordinate frame
"""
tmp = CoordinateFrameResource(name=self.experiment.coord_frame)
coor = self.rmt.get_project(tmp)
self.coordinate_frame = coor
return coor
def get_all(self):
"""
:return: the entire channel image data at its native resolution
"""
x_rng = [self.coordinate_frame.x_start, self.coordinate_frame.x_stop]
y_rng = [self.coordinate_frame.y_start, self.coordinate_frame.y_stop]
z_rng = [self.coordinate_frame.z_start, self.coordinate_frame.z_stop]
return self.rmt.get_cutout(self.channel, 0, x_rng, y_rng, z_rng)
def get_cutout(self, x_range, y_range, z_range, resolution=0):
"""
:return: a cutout of the image data
"""
return self.rmt.get_cutout(self.channel, resolution, x_range, y_range,
z_range)
print(coll_list)
boss_url = 'https://api.boss.neurodata.io/v1'
url_constr = boss_url + '/collection/{}/experiment/{}/channel/{}'
config = configparser.ConfigParser()
config.read(boss_config_file)
APITOKEN = config['Default']['token']
headers = {'Authorization': 'Token {}'.format(APITOKEN)}
s = requests.Session()
#%%
data = []
for coll in coll_list:
exp_list = rmt.list_experiments(coll)
for exp in exp_list:
ch_list = rmt.list_channels(coll, exp)
for ch in ch_list:
url = '{}/downsample/{}/{}/{}'.format(boss_url, coll, exp, ch)
r = s.get(url, headers=headers)
try:
downsample_resp = r.json()
downsample_status = downsample_resp['status']
extent = downsample_resp['extent']
last_extent = extent[sorted(extent.keys())[-1]]
first_extent = extent[sorted(extent.keys())[0]]
data.append([
from intern.remote.boss import BossRemote
from intern.resource.boss.resource import *
# admin token needed to list all projects
rmt = BossRemote("/home/ben/Documents/travis_user_neurodata.cfg")
with open("public_datasets.csv", "w") as f:
f.write(
"coll,exp,ch,exp_description,num_hierarchy_levels,dtype,x_start,x_stop,y_start,y_stop,z_start,z_stop\n"
)
colls = rmt.list_collections()
colls.remove("ben_dev")
colls.remove("ZBrain")
for coll in colls:
exps = rmt.list_experiments(coll)
for exp in exps:
exp_res = rmt.get_experiment(coll, exp)
coord_frame_res = rmt.get_coordinate_frame(exp_res.coord_frame)
chs = rmt.list_channels(coll, exp)
for ch in chs:
ch_res = rmt.get_channel(ch, coll, exp)
with open("public_datasets.csv", "a") as f:
f.write(
f"{coll},{exp},{ch},{exp_res.description},{exp_res.num_hierarchy_levels},{ch_res.datatype},{coord_frame_res.x_start},{coord_frame_res.x_stop},{coord_frame_res.y_start},{coord_frame_res.y_stop},{coord_frame_res.z_start},{coord_frame_res.z_stop}\n"
)
class ProjectServiceTest_v1(unittest.TestCase):
"""Integration tests of the Boss resource API.
"""
def setUp(self):
self.rmt = BossRemote('test.cfg', API_VER)
# Turn off SSL cert verification. This is necessary for interacting with
# developer instances of the Boss.
self.rmt.project_service.session_send_opts = {'verify': False}
self.rmt.metadata_service.session_send_opts = {'verify': False}
self.rmt.volume_service.session_send_opts = {'verify': False}
requests.packages.urllib3.disable_warnings(InsecureRequestWarning)
coll_name = 'collection2309-{}'.format(random.randint(0, 9999))
self.coll = CollectionResource(coll_name, 'bar')
coll_name_upd = '{}-{}'.format(coll_name, random.randint(0, 9999))
self.coll_upd = CollectionResource(coll_name_upd, 'latest')
cf_name = 'ProjTestFrame{}'.format(random.randint(0, 9999))
self.coord = CoordinateFrameResource(cf_name, 'Test coordinate frame.',
0, 10, -5, 5, 3, 6, 1, 1, 1,
'nanometers')
self.coord_upd = copy.copy(self.coord)
self.coord_upd.name = 'MouseFrame{}'.format(random.randint(0, 9999))
self.coord_upd.description = 'Mouse coordinate frame.'
self.exp = ExperimentResource('exp2309-2',
self.coll.name,
self.coord.name,
'my experiment',
1,
'isotropic',
time_step=2,
time_step_unit='nanoseconds')
self.exp_upd = ExperimentResource('exp2309-2a', self.coll.name,
self.coord.name,
'my first experiment', 2,
'anisotropic')
self.source_chan = ChannelResource('sourceChan', self.coll.name,
self.exp.name, 'image',
'test source channel', 0, 'uint8',
0)
self.related_chan = ChannelResource('relatedChan', self.coll.name,
self.exp.name, 'image',
'test related channel', 0, 'uint8',
0)
self.chan = ChannelResource('myChan',
self.coll.name,
self.exp.name,
'annotation',
'test annotation channel',
0,
'uint8',
0,
sources=['sourceChan'],
related=['relatedChan'])
self.chan_upd = ChannelResource('yourChan',
self.coll.name,
self.exp.name,
'annotation',
'your test annotation channel',
0,
'uint8',
1,
sources=['sourceChan'],
related=['relatedChan'])
def tearDown(self):
try:
self.rmt.delete_project(self.chan_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.chan)
except HTTPError:
pass
try:
self.rmt.delete_project(self.related_chan)
except HTTPError:
pass
try:
self.rmt.delete_project(self.source_chan)
except HTTPError:
pass
try:
self.rmt.delete_project(self.exp_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.exp)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coord_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coord)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coll_upd)
except HTTPError:
pass
try:
self.rmt.delete_project(self.coll)
except HTTPError:
pass
def test_create_coord_frame(self):
cf = self.rmt.create_project(self.coord)
self.assertEqual(self.coord.name, cf.name)
self.assertEqual(self.coord.description, cf.description)
self.assertEqual(self.coord.x_start, cf.x_start)
self.assertEqual(self.coord.x_stop, cf.x_stop)
self.assertEqual(self.coord.y_start, cf.y_start)
self.assertEqual(self.coord.y_stop, cf.y_stop)
self.assertEqual(self.coord.z_start, cf.z_start)
self.assertEqual(self.coord.z_stop, cf.z_stop)
self.assertEqual(self.coord.x_voxel_size, cf.x_voxel_size)
self.assertEqual(self.coord.y_voxel_size, cf.y_voxel_size)
self.assertEqual(self.coord.z_voxel_size, cf.z_voxel_size)
self.assertEqual(self.coord.voxel_unit, cf.voxel_unit)
def test_create_collection(self):
c = self.rmt.create_project(self.coll)
self.assertEqual(self.coll.name, c.name)
self.assertEqual(self.coll.description, c.description)
def test_create_experiment(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
self.assertEqual(self.exp.name, e.name)
self.assertEqual(self.exp.description, e.description)
self.assertEqual(self.coll.name, e.coll_name)
self.assertEqual(self.exp.coord_frame, e.coord_frame)
self.assertEqual(self.exp.hierarchy_method, e.hierarchy_method)
self.assertEqual(self.exp.num_hierarchy_levels, e.num_hierarchy_levels)
self.assertEqual(self.exp.num_time_samples, e.num_time_samples)
self.assertEqual(self.exp.time_step, e.time_step)
self.assertEqual(self.exp.time_step_unit, e.time_step_unit)
def test_create_channel(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
ch = self.rmt.create_project(self.source_chan)
self.assertEqual(self.source_chan.name, ch.name)
self.assertEqual(self.exp.name, ch.exp_name)
self.assertEqual(self.source_chan.description, ch.description)
self.assertEqual(self.coll.name, ch.coll_name)
self.assertEqual(self.source_chan.datatype, ch.datatype)
self.assertEqual(self.source_chan.default_time_sample,
ch.default_time_sample)
self.assertEqual(self.source_chan.base_resolution, ch.base_resolution)
def test_create_annotation_channel_without_source_fails(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
rel_ch = self.rmt.create_project(self.related_chan)
chan = ChannelResource('myChan',
self.coll.name,
self.exp.name,
'annotation',
'test annotation channel',
0,
'uint8',
0,
related=['relatedChan'])
with self.assertRaises(HTTPError):
self.rmt.create_project(chan)
def test_create_annotation_channel(self):
"""Annotation channels require a source channel."""
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
ch = self.rmt.create_project(self.source_chan)
rel_ch = self.rmt.create_project(self.related_chan)
ann_ch = self.rmt.create_project(self.chan)
self.assertEqual(self.chan.name, ann_ch.name)
self.assertEqual(self.exp.name, ann_ch.exp_name)
self.assertEqual(self.chan.description, ann_ch.description)
self.assertEqual(self.coll.name, ann_ch.coll_name)
self.assertEqual(self.chan.datatype, ann_ch.datatype)
self.assertEqual(self.chan.default_time_sample,
ann_ch.default_time_sample)
self.assertEqual(self.chan.base_resolution, ann_ch.base_resolution)
self.assertEqual(self.chan.sources, ann_ch.sources)
self.assertEqual(self.chan.related, ann_ch.related)
def test_get_collection(self):
coll = self.rmt.create_project(self.coll)
c = self.rmt.get_project(self.coll)
self.assertEqual(self.coll.name, c.name)
self.assertEqual(self.coll.description, c.description)
def test_get_coord_frame(self):
coord = self.rmt.create_project(self.coord)
cf = self.rmt.get_project(self.coord)
self.assertEqual(self.coord.name, cf.name)
self.assertEqual(self.coord.description, cf.description)
self.assertEqual(self.coord.x_start, cf.x_start)
self.assertEqual(self.coord.x_stop, cf.x_stop)
self.assertEqual(self.coord.y_start, cf.y_start)
self.assertEqual(self.coord.y_stop, cf.y_stop)
self.assertEqual(self.coord.z_start, cf.z_start)
self.assertEqual(self.coord.z_stop, cf.z_stop)
self.assertEqual(self.coord.x_voxel_size, cf.x_voxel_size)
self.assertEqual(self.coord.y_voxel_size, cf.y_voxel_size)
self.assertEqual(self.coord.z_voxel_size, cf.z_voxel_size)
self.assertEqual(self.coord.voxel_unit, cf.voxel_unit)
def test_get_experiment(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
exp = self.rmt.create_project(self.exp)
e = self.rmt.get_project(self.exp)
self.assertEqual(self.exp.name, e.name)
self.assertEqual(self.exp.description, e.description)
self.assertEqual(self.coll.name, e.coll_name)
self.assertEqual(self.exp.coord_frame, e.coord_frame)
self.assertEqual(self.exp.hierarchy_method, e.hierarchy_method)
self.assertEqual(self.exp.num_hierarchy_levels, e.num_hierarchy_levels)
self.assertEqual(self.exp.num_time_samples, e.num_time_samples)
self.assertEqual(self.exp.time_step, e.time_step)
self.assertEqual(self.exp.time_step_unit, e.time_step_unit)
def test_get_channel(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
chan = self.rmt.create_project(self.source_chan)
ch = self.rmt.get_project(self.source_chan)
self.assertEqual(self.source_chan.name, ch.name)
self.assertEqual(self.exp.name, ch.exp_name)
self.assertEqual(self.source_chan.description, ch.description)
self.assertEqual(self.coll.name, ch.coll_name)
self.assertEqual(self.source_chan.datatype, ch.datatype)
self.assertEqual(self.source_chan.default_time_sample,
ch.default_time_sample)
self.assertEqual(self.source_chan.base_resolution, ch.base_resolution)
def test_get_channel_helper(self):
"""
Test the helper get_channel() as opposed to getting a channel via get_project().
"""
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
chan = self.rmt.create_project(self.source_chan)
actual = self.rmt.get_channel(chan.name, chan.coll_name, chan.exp_name)
# This is not an exhaustive list of attributes, but they are the
# important ones for correct interaction with the volume service.
self.assertTrue(actual.cutout_ready)
self.assertEqual(chan.datatype, actual.datatype)
self.assertEqual(chan.default_time_sample, actual.default_time_sample)
self.assertEqual(chan.base_resolution, actual.base_resolution)
self.assertEqual(chan.downsample_status, actual.downsample_status)
self.assertEqual(chan.type, actual.type)
self.assertEqual(chan.name, actual.name)
self.assertEqual(chan.coll_name, actual.coll_name)
self.assertEqual(chan.exp_name, actual.exp_name)
def test_update_collection(self):
coll = self.rmt.create_project(self.coll)
c = self.rmt.update_project(self.coll.name, self.coll_upd)
self.assertEqual(self.coll_upd.name, c.name)
self.assertEqual(self.coll_upd.description, c.description)
def test_update_coord_frame(self):
c = self.rmt.create_project(self.coll)
coord = self.rmt.create_project(self.coord)
cf = self.rmt.update_project(self.coord.name, self.coord_upd)
self.assertEqual(self.coord_upd.name, cf.name)
self.assertEqual(self.coord_upd.description, cf.description)
def test_update_experiment(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
eup = self.rmt.update_project(self.exp.name, self.exp_upd)
self.assertEqual(self.exp_upd.name, eup.name)
self.assertEqual(self.exp_upd.description, eup.description)
self.assertEqual(self.coll.name, eup.coll_name)
self.assertEqual(self.exp_upd.coord_frame, eup.coord_frame)
self.assertEqual(self.exp_upd.hierarchy_method, eup.hierarchy_method)
self.assertEqual(self.exp_upd.num_hierarchy_levels,
eup.num_hierarchy_levels)
self.assertEqual(self.exp_upd.num_time_samples, eup.num_time_samples)
self.assertEqual(self.exp.time_step, eup.time_step)
self.assertEqual(self.exp.time_step_unit, eup.time_step_unit)
def test_update_channel(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
source_ch = self.rmt.create_project(self.source_chan)
rel_ch = self.rmt.create_project(self.related_chan)
chan = self.rmt.create_project(self.chan)
ch = self.rmt.update_project(self.chan.name, self.chan_upd)
self.assertEqual(self.chan_upd.name, ch.name)
self.assertEqual(self.exp.name, ch.exp_name)
self.assertEqual(self.chan_upd.description, ch.description)
self.assertEqual(self.coll.name, ch.coll_name)
self.assertEqual(self.chan_upd.datatype, ch.datatype)
self.assertEqual(self.chan_upd.default_time_sample,
ch.default_time_sample)
self.assertEqual(self.chan_upd.base_resolution, ch.base_resolution)
self.assertEqual(self.chan_upd.sources, ch.sources)
self.assertEqual(self.chan_upd.related, ch.related)
def test_list_collections(self):
coll = self.rmt.create_project(self.coll)
coll_list = self.rmt.list_collections()
c = [name for name in coll_list if name == self.coll.name]
self.assertEqual(1, len(c))
self.assertEqual(self.coll.name, c[0])
def test_list_coord_frames(self):
cf = self.rmt.create_project(self.coord)
cf_list = self.rmt.list_coordinate_frames()
c = [name for name in cf_list if name == self.coord.name]
self.assertEqual(1, len(c))
self.assertEqual(self.coord.name, c[0])
def test_list_experiments(self):
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
exp = self.rmt.create_project(self.exp)
exp_list = self.rmt.list_experiments(self.coll.name)
e = [name for name in exp_list if name == self.exp.name]
self.assertEqual(1, len(e))
self.assertEqual(self.exp.name, e[0])
#def test_list_channels(self):
# c = self.rmt.create_project(self.coll)
# cf = self.rmt.create_project(self.coord)
# e = self.rmt.create_project(self.exp)
# chan = self.rmt.create_project(self.chan)
# chan_list = self.rmt.list_channels(self.coll.name, self.exp.name)
# ch = [name for name in chan_list if name == self.chan.name]
# self.assertEqual(1, len(ch))
# self.assertEqual(self.chan.name, ch[0])
def test_delete_all(self):
"""Formally test delete at all levels of the data model.
Delete happens all the time in the tearDown() but specifically test
it here.
"""
c = self.rmt.create_project(self.coll)
cf = self.rmt.create_project(self.coord)
e = self.rmt.create_project(self.exp)
ch = self.rmt.create_project(self.source_chan)
self.rmt.delete_project(self.source_chan)
self.rmt.delete_project(self.exp)
self.rmt.delete_project(self.coord)
self.rmt.delete_project(self.coll)
def gen_urls(args):
config = {'protocol': 'https',
'host': args.hostname,
'token': args.token}
boss = BossRemote(config)
results = []
try:
if args.collection is not None:
collections = [args.collection]
else:
collections = boss.list_collections()
for collection in collections:
if args.experiment is not None:
experiments = [args.experiment]
else:
experiments = boss.list_experiments(collection)
for experiment in experiments:
if args.channel is not None:
channels = [args.channel]
else:
channels = boss.list_channels(collection, experiment)
exp = ExperimentResource(name = experiment,
collection_name = collection)
exp = boss.get_project(exp)
coord = CoordinateFrameResource(name = exp.coord_frame)
coord = boss.get_project(coord)
for channel in channels:
ch = ChannelResource(name = channel,
experiment_name = experiment,
collection_name = collection)
ch = boss.get_project(ch)
def check_range(name, var, start, stop):
start_, stop_ = map(int, var.split(':'))
if start_ < start:
fmt = "{} range start for {}/{}/{} is less than the coordinate frame, setting to minimum"
print(fmt.format(name, collection, experiment, channel))
start_ = start
if stop_ > stop:
fmt = "{} range stop for {}/{}/{} is greater than the coordinate frame, setting to maximum"
print(fmt.format(name, collection, experiment, channel))
stop_ = stop
return '{}:{}'.format(start_, stop_)
if args.x_range:
x = check_range('X', args.x_range, coord.x_start, coord.x_stop)
else:
x = (coord.x_start, coord.x_stop, args.min, args.max)
if args.y_range:
y = check_range('Y', args.y_range, coord.y_start, coord.y_stop)
else:
y = (coord.y_start, coord.y_stop, args.min, args.max)
if args.z_range:
z = check_range('Z', args.z_range, coord.z_start, coord.z_stop)
else:
z = (coord.z_start, coord.z_stop, args.min, args.max)
# Arguments to gen_url
results.append((args.hostname,
collection,
experiment,
channel,
0, x, y, z, None))
except Exception as e:
print("Error generating URLs: {}".format(e))
return results
