def test_get_chromosome_00():
"""
Test the list of chromosomes when no resolution has been specied is zero
"""
hdf5_handle = coord('test', '')
chromosomes = hdf5_handle.get_chromosomes()
chromosomes_count = len(chromosomes)
assert chromosomes_count == 0
def test_resolutions():
"""
Test to get a list of the available resolutions that models have been
generated for
"""
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
results_count = len(results)
assert results_count > 0
def test_get_regions():
"""
Test that there are regions returned when querying a given chromosome with a
start and end value
"""
print("test_get_regions")
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
hdf5_handle.set_resolution(int(results[0]))
results = get_region_ids(hdf5_handle)
print('\tGet Regions:', len(results))
assert results is not None
def test_set_resolution():
"""
Test to set the resolution and ensure that the value has been updated in the
object
"""
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
res_before = hdf5_handle.get_resolution()
hdf5_handle.set_resolution(int(results[0]))
res_after = hdf5_handle.get_resolution()
assert res_before is None
assert res_after == int(results[0])
def test_object_data():
"""
Test getting the header data for the JSON object
"""
print("test_object_data")
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
hdf5_handle.set_resolution(int(results[0]))
region_ids = get_region_ids(hdf5_handle, True)
results = hdf5_handle.get_object_data(region_ids['region_ids'][0])
print('\tObject Data:', results)
assert 'assembly' in results
def test_get_chromosome_01():
"""
Test that the list of chromosomes has values when the resolution is
specified
"""
print("test_get_chromosome_01")
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
hdf5_handle.set_resolution(int(results[0]))
chromosomes = hdf5_handle.get_chromosomes()
print("\tChromosomes:", chromosomes)
assert chromosomes
def test_get_model():
"""
Test getting a model for a given region and model ID
"""
print("test_get_model")
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
hdf5_handle.set_resolution(int(results[0]))
region_ids = get_region_ids(hdf5_handle, True)
models = hdf5_handle.get_models(region_ids['region_ids'][0])
results = hdf5_handle.get_model(region_ids['region_ids'][0], models[0])
print('\tModel:', results[0]['object'])
assert 'object' in results[0]
def test_get_models():
"""
Test getting the list of models for a given region
"""
print("test_get_models")
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
hdf5_handle.set_resolution(int(results[0]))
region_ids = get_region_ids(hdf5_handle, True)
results = hdf5_handle.get_models(region_ids['region_ids'][0])
print('\tModels:', len(results))
models_count = len(results)
assert models_count == 1000
def test_centroids():
"""
Test getting the list of centroids
"""
print("test_centroids")
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
hdf5_handle.set_resolution(int(results[0]))
region_ids = get_region_ids(hdf5_handle, True)
results = hdf5_handle.get_centroids(region_ids['region_ids'][0])
print('\tCentroids:', results)
centroid_count = len(results)
assert centroid_count == 5
def test_get_region_order():
"""
Test the ordering of models given a chromosome, start and end parameter
"""
print("test_get_region_order")
hdf5_handle = coord('test', '')
results = hdf5_handle.get_resolutions()
hdf5_handle.set_resolution(int(results[0]))
region_ids = get_region_ids(hdf5_handle, True)
print('\tRegion Order:', region_ids)
results = hdf5_handle.get_region_order(region_ids['chromosome'],
region_ids['region_ids'][0])
print('\tRegion Order:', results)
assert results is not None
