def test_complex_json(self):
"""Test the complex JSON project creation with only the required fields"""
p.token = 'unittest2'
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [2000,2000,30], [1.0,1.0,5.0], [0,0,0], None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = { p.channels[1] : (p.channels[1], p.datatype, p.channel_type, 'sample_data_url', 'sample_filename', 'tif', None, None, None, None) }
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(createJson(dataset, project, channels))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(postURL("http://{}/ca/autoIngest/".format(SITE_HOST), json_file).read())
assert('SUCCESS. The ingest process has now started.' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert( proj_info['project']['name'] == p.token )
assert( proj_info['dataset']['imagesize']['0'] == [2000,2000,30])
assert( proj_info['dataset']['cube_dimension']['0'] == [128,128,16])
assert( proj_info['dataset']['scalinglevels'] == 1)
assert( proj_info['channels'][p.channels[1]]['resolution'] == 0)
assert( proj_info['channels'][p.channels[1]]['datatype'] == p.datatype)
def test_error_json(self):
"""Test the wrong JSON channel creation with only the required fields"""
# Here we send incorrect dataset information
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [1000, 2000, 1000], [1.0, 1.0,
5.0], [0, 0,
0], None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = {
p.channels[1]:
(p.channels[1], p.datatype, p.channel_type, 'sample_data_url',
'sample_filename', 'tif', None, None, None, None)
}
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(
createJson(dataset, project, channels, channel_only=True))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(
postURL(
"http://{}/ca/{}/createChannel/".format(SITE_HOST, p.token),
json_file).read())
assert ('FAILED' == response)
def test_create_json(self):
"""Test the basic JSON project creation with only the required fields"""
p.channels = ['CHAN1', 'CHAN2']
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [2000, 2000,
1000], [1.0, 1.0, 5.0], None, None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = {
p.channels[0]:
(p.channels[0], p.datatype, p.channel_type, 'sample_data_url',
'sample_filename', 'tif', None, None, None, 0),
p.channels[1]:
(p.channels[1], p.datatype, p.channel_type, 'sample_data_url',
'sample_filename', 'tif', None, None, None, 0),
}
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(
createJson(dataset, project, channels, channel_only=True))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(
postURL(
"http://{}/ca/{}/createChannel/".format(SITE_HOST, p.token),
json_file).read())
assert (
'SUCCESS. The information in the channel was correct.' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert (proj_info['project']['name'] == p.token)
assert (proj_info['dataset']['imagesize']['0'] == [2000, 2000, 1000])
assert (proj_info['dataset']['cube_dimension']['0'] == [128, 128, 16])
assert (proj_info['dataset']['scalinglevels'] == 5)
assert (proj_info['channels'][p.channels[0]]['resolution'] == 0)
assert (proj_info['channels'][p.channels[0]]['channel_type'] ==
p.channel_type)
assert (proj_info['channels'][p.channels[1]]['datatype'] == p.datatype)
# Testing if the it allows data to be posted to the created channels
p.args = (1000, 1100, 500, 600, 200, 201)
image_data = np.ones([2, 1, 100, 100],
dtype=np.uint8) * random.randint(0, 255)
response = postNPZ(p, image_data)
voxarray = getNPZ(p)
assert (np.array_equal(image_data, voxarray))
def test_basic_json(self):
"""Test the basic JSON project creation with only the required fields"""
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [2000, 2000, 30], [1.0, 1.0,
5.0], None, None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = {
p.channels[0]: (p.channels[0], p.datatype, p.channel_type,
'http://127.0.0.1/data/sample_dir/', 'SLICE',
'tif', None, None, None, None)
}
metadata = {
'Author': 'Will',
'Animal': 'Mouse',
'Date_Collected': '10/2/2015'
}
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(
createJson(dataset, project, channels, metadata=metadata))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(
postURL("http://{}/ca/createProject/".format(SITE_HOST),
json_file).read())
assert ('SUCCESS' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert (proj_info['project']['name'] == p.token)
assert (proj_info['dataset']['imagesize']['0'] == [2000, 2000, 30])
assert (proj_info['dataset']['cube_dimension']['0'] == [128, 128, 16])
assert (proj_info['dataset']['scalinglevels'] == 1)
assert (proj_info['channels'][p.channels[0]]['resolution'] == 0)
assert (proj_info['channels'][p.channels[0]]['datatype'] == p.datatype)
try:
assert (proj_info['metadata'][0]['Author'] == 'Will')
except KeyError:
print "LIMS System not working"
except AssertionError:
print "LIMS System not working"
def test_error_json(self):
"""Test the wrong JSON channel creation with only the required fields"""
# Here we send incorrect dataset information
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [1000,2000,1000], [1.0,1.0,5.0], [0,0,0], None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = { p.channels[1] : (p.channels[1], p.datatype, p.channel_type, 'sample_data_url', 'sample_filename', 'tif', None, None, None, None) }
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(createJson(dataset, project, channels, channel_only=True))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(postURL("http://{}/ca/{}/createChannel/".format(SITE_HOST, p.token), json_file).read())
assert('Channel CHAN2 already exists for this project. Specify a different channel name' == response)
def test_single_channel_json(self):
"""Test the basic JSON project creation with only the required fields"""
ocp_dict = { 'channels' : (p.channels[1],) }
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(json.dumps(ocp_dict, sort_keys=True, indent=4))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(postURL("http://{}/ca/{}/deleteChannel/".format(SITE_HOST, p.token), json_file).read())
assert('SUCCESS' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert( proj_info['project']['name'] == p.token )
assert( proj_info['channels'][p.channels[0]]['resolution'] == 0)
def test_create_json(self):
"""Test the basic JSON project creation with only the required fields"""
p.channels = ['CHAN1', 'CHAN2']
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [2000,2000,1000], [1.0,1.0,5.0], None, None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = { p.channels[0] : (p.channels[0], p.datatype, p.channel_type, 'sample_data_url', 'sample_filename', 'tif', None, None, None, 0), p.channels[1] : (p.channels[1], p.datatype, p.channel_type, 'sample_data_url', 'sample_filename', 'tif', None, None, None, 0), }
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(createJson(dataset, project, channels, channel_only=True))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(postURL("http://{}/ca/{}/createChannel/".format(SITE_HOST, p.token), json_file).read())
assert('SUCCESS. The information in the channel was correct.' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert( proj_info['project']['name'] == p.token )
assert( proj_info['dataset']['imagesize']['0'] == [2000,2000,1000])
assert( proj_info['dataset']['cube_dimension']['0'] == [128,128,16])
assert( proj_info['dataset']['scalinglevels'] == 5)
assert( proj_info['channels'][p.channels[0]]['resolution'] == 0)
assert( proj_info['channels'][p.channels[0]]['channel_type'] == p.channel_type)
assert( proj_info['channels'][p.channels[1]]['datatype'] == p.datatype)
# Testing if the it allows data to be posted to the created channels
p.args = (1000,1100,500,600,200,201)
image_data = np.ones( [2,1,100,100], dtype=np.uint8 ) * random.randint(0,255)
response = postNPZ(p, image_data)
voxarray = getNPZ(p)
assert( np.array_equal(image_data, voxarray) )
def test_complex_json(self):
"""Test the complex JSON project creation with only the required fields"""
p.token = 'unittest2'
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [2000, 2000, 30], [1.0, 1.0,
5.0], [0, 0,
0], None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = {
p.channels[1]:
(p.channels[1], p.datatype, p.channel_type, 'sample_data_url',
'sample_filename', 'tif', None, None, None, None)
}
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(createJson(dataset, project, channels))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(
postURL("http://{}/ca/createProject/".format(SITE_HOST),
json_file).read())
assert ('SUCCESS' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert (proj_info['project']['name'] == p.token)
assert (proj_info['dataset']['imagesize']['0'] == [2000, 2000, 30])
assert (proj_info['dataset']['cube_dimension']['0'] == [128, 128, 16])
assert (proj_info['dataset']['scalinglevels'] == 1)
assert (proj_info['channels'][p.channels[1]]['resolution'] == 0)
assert (proj_info['channels'][p.channels[1]]['datatype'] == p.datatype)
def test_single_channel_json(self):
"""Test the basic JSON project creation with only the required fields"""
ocp_dict = {'channels': (p.channels[1], )}
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(json.dumps(ocp_dict, sort_keys=True, indent=4))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(
postURL(
"http://{}/ca/{}/deleteChannel/".format(SITE_HOST, p.token),
json_file).read())
assert ('SUCCESS' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert (proj_info['project']['name'] == p.token)
assert (proj_info['channels'][p.channels[0]]['resolution'] == 0)
def test_basic_json(self):
"""Test the basic JSON project creation with only the required fields"""
# dataset format = (dataset_name, [ximagesz, yimagesz, zimagesz], [[xvoxel, yvoxel, zvoxel], [xoffset, yoffset, zoffset], timerange, scalinglevels, scaling)
dataset = (p.dataset, [2000,2000,30], [1.0,1.0,5.0], None, None, None, None)
# project format = (project_name, token_name, public)
project = (p.token, None, None)
# channel format = { chan1 : (channel_name, datatype, channel_type, data_url, file_name, exceptions, resolution, windowrange, readonly), chan2: ...... }
channels = { p.channels[0] : (p.channels[0], p.datatype, p.channel_type, 'http://127.0.0.1/data/sample_dir/', 'SLICE', 'tif', None, None, None, None) }
metadata = { 'Author': 'Will', 'Animal':'Mouse', 'Date_Collected':'10/2/2015' }
json_file = tempfile.NamedTemporaryFile(mode='w+b')
json_file.write(createJson(dataset, project, channels, metadata=metadata))
json_file.seek(0)
# posting the JSON url and checking if it is successful
response = json.loads(postURL("http://{}/ca/autoIngest/".format(SITE_HOST), json_file).read())
assert('SUCCESS. The ingest process has now started.' == response)
# fetching the JSON info
f = getURL("http://{}/ca/{}/info/".format(SITE_HOST, p.token))
# read the JSON file
proj_info = json.loads(f.read())
assert( proj_info['project']['name'] == p.token )
assert( proj_info['dataset']['imagesize']['0'] == [2000,2000,30])
assert( proj_info['dataset']['cube_dimension']['0'] == [128,128,16])
assert( proj_info['dataset']['scalinglevels'] == 1)
assert( proj_info['channels'][p.channels[0]]['resolution'] == 0)
assert( proj_info['channels'][p.channels[0]]['datatype'] == p.datatype)
try:
assert( proj_info['metadata'][0]['Author'] == 'Will')
except KeyError:
print "LIMS System not working"
except AssertionError:
print "LIMS System not working"