def test_good_databasic(array, location, mappings):
data = spatial.DataBasic(
array=array,
location=location,
mappings=mappings,
)
assert data.validate()
def translate_data_array(steno3d_data, location, view, _lookup_dict=None):
"""Translate Steno3D array data into Data, Mapping, and Arrays"""
arr = files.Array(steno3d_data.array)
data = spatial.DataBasic(
name=steno3d_data.title or '',
description=steno3d_data.description or '',
array=arr,
location=location,
)
if steno3d_data.colormap is not None:
gradient = files.Array(steno3d_data.colormap)
mapping = spatial.MappingContinuous(
gradient=gradient,
data_controls=[
np.nanmin(steno3d_data.array),
np.nanmax(steno3d_data.array),
],
gradient_controls=[0., 1.],
visibility=[True, True, True],
)
data.mappings = [mapping]
view.contents += [mapping, gradient]
view.contents += [arr, data]
if _lookup_dict is not None and hasattr(steno3d_data, '_upload_data'):
_lookup_dict.update({steno3d_data._upload_data['uid']: data})
return data
def translate_data_discrete(steno3d_data, location, view, _lookup_dict=None):
"""Translate Steno3D discrete data into Data, Mapping, and Array"""
arr = files.Array(steno3d_data.array)
if steno3d_data.range_visibility is not None:
visibility = [bool(rv) for rv in steno3d_data.range_visibility]
else:
visibility = [True] * (len(steno3d_data.end_values) + 1)
if steno3d_data.end_inclusive is not None:
end_inclusive = [bool(ei) for ei in steno3d_data.end_inclusive]
else:
end_inclusive = [True] * len(steno3d_data.end_values)
mapping = spatial.MappingDiscrete(
end_points=steno3d_data.end_values,
visibility=visibility,
end_inclusive=end_inclusive,
values=steno3d_data.colormap
or [''] * (len(steno3d_data.end_values) + 1),
)
data = spatial.DataBasic(name=steno3d_data.title or '',
description=steno3d_data.description or '',
array=arr,
location=location,
mappings=[mapping])
view.contents += [arr, mapping, data]
if _lookup_dict is not None and hasattr(steno3d_data, '_upload_data'):
_lookup_dict.update({steno3d_data._upload_data['uid']: data})
return data
def test_sanitize_colormaps():
data = spatial.DataBasic()
data = utils.sanitize_data_colormaps(data)
assert len(data.mappings) == 0
data.mappings = [spatial.MappingContinuous()]
data = utils.sanitize_data_colormaps(data)
assert len(data.mappings) == 1
data.mappings = [
spatial.MappingDiscrete(values=[1., 2, 3]),
spatial.MappingContinuous(),
spatial.MappingDiscrete(values=['r', 'g', 'b']),
]
data = utils.sanitize_data_colormaps(data)
assert len(data.mappings) == 3
assert data.mappings[0].values == [(255, 0, 0), (0, 255, 0), (0, 0, 255)]
assert data.mappings[1].values == [1., 2, 3]
assert isinstance(data.mappings[2], spatial.MappingContinuous)
data = spatial.DataCategory(
categories=
'https://example.com/api/v1/view/org1/proj1/view1/mappings/category/abc123',
)
data = utils.sanitize_data_colormaps(data)
assert len(data.mappings) == 1
assert data.mappings[0] == data.categories
data.mappings = [spatial.MappingCategory(values=[1., 2, 3])]
data.categories = spatial.MappingCategory(values=[1., 2, 3])
data = utils.sanitize_data_colormaps(data)
assert len(data.mappings) == 2
assert isinstance(data.mappings[0].values[0], tuple)
assert data.mappings[1].values == [1., 2, 3]
def test_bad_databasic(prop, bad_val):
data = spatial.DataBasic(
array='https://example.com/api/files/array/abc123',
location='N',
)
with pytest.raises(properties.ValidationError):
setattr(data, prop, bad_val)
data.validate()
def test_extra_slide_validation():
element_list = [
'https://example.com/api/v1/view/org1/proj1/view1/elements/pointset/abc123',
'https://example.com/api/v1/view/org1/proj1/view1/elements/surface/def456',
]
slide = scene.Slide(scene=scene.Scene())
slide.scene.plots[0].views = [
scene.PointSet(element=spatial.ElementPointSet())
]
with pytest.raises(properties.ValidationError):
utils.extra_slide_validation(slide, element_list)
slide.scene.plots[0].views = [
scene.PointSet(
element=
'https://example.com/api/v1/view/org1/proj1/view1/elements/pointset/abc123',
)
]
with pytest.raises(properties.ValidationError):
utils.extra_slide_validation(slide, element_list)
slide.scene.plots[0].views = [
scene.PointSet(
element=
'https://example.com/api/v1/view/org1/proj1/view1/elements/pointset/abc123',
),
scene.Surface(
element=
'https://example.com/api/v1/view/org1/proj1/view1/elements/surface/def456',
)
]
utils.extra_slide_validation(slide, element_list)
slide.scene.plots[0].views[
0].color.mapping = 'https://example.com/api/v1/view/org1/proj1/view1/mappings/continuous/def456'
slide.scene.plots[0].views[0].color.data = spatial.DataBasic()
with pytest.raises(properties.ValidationError):
utils.extra_slide_validation(slide, element_list)
slide.scene.plots[0].views[0].color.mapping = properties.undefined
slide.scene.plots[0].views[0].color.data = properties.undefined
slide.scene.plots[0].views[1].textures = [{
'data':
spatial.TextureProjection(),
}]
with pytest.raises(properties.ValidationError):
utils.extra_slide_validation(slide, element_list)
def test_upload(mock_regex, mock_upload_image, mock_upload_array, mock_put,
mock_patch, mock_post, verbose, workers, parallel, session):
mock_resp = mock.MagicMock()
mock_resp.json.return_value = {
'links': {
'self': 'https://example.com/api/self',
'location': 'https://example.com/api/location',
'thumbnail': 'https://example.com/api/self/thumbnail'
},
}
mock_resp.ok = True
mock_post.return_value = mock_resp
mock_patch.return_value = mock_resp
mock_put.return_value = mock_resp
mock_file_resp = mock.MagicMock()
mock_file_resp.json.return_value = {}
mock_file_resp.ok = True
mock_upload_array.return_value = mock_file_resp
mock_upload_image.return_value = mock_file_resp
mock_regex.return_value = re.compile(r'^https://example\.com/api/')
mapping_uploaded = spatial.MappingDiscrete(
values=[(255, 0, 0), (0, 255, 0), (0, 0, 255)],
end_points=[10., 20.],
end_inclusive=[True, True],
visibility=[True, True, True],
)
mapping_uploaded._links = {
'self': 'https://example.com/api/mapping_uploaded'
}
array_data = files.Array([0., 10, 20])
img = io.BytesIO()
s = [[0, 1, 0, 1], [1, 0, 1, 0], [0, 1, 0, 1], [1, 0, 1, 0]]
w = png.Writer(4, 4, greyscale=True, bitdepth=16)
w.write(img, s)
view = manifests.View(
name='Test View',
elements=[
spatial.ElementPointSet(
vertices=files.Array([[0., 0, 0], [1, 1, 1], [2, 2, 2]]),
data=[
spatial.DataBasic(
name='Dataset 1',
location='n',
array=array_data,
uid='local_id',
),
spatial.DataBasic(
name='Dataset 2',
description='Same array as dataset 1',
location='n',
array=array_data,
mappings=[
spatial.MappingContinuous(
gradient='https://example.com/api/my_colormap',
data_controls=[0., 10., 20., 30.],
),
mapping_uploaded,
]),
spatial.TextureProjection(
origin=[0., 0, 0],
axis_u=[1., 0, 0],
axis_v=[0., 1, 0],
image=img,
),
],
defaults={
'color': {
'value': '#FF0000'
},
'opacity': {
'value': 1
},
'size': {
'value': 10
},
'shape': 'square'
},
),
'https://example.com/api/my_element',
])
try:
dirname, _ = os.path.split(os.path.abspath(__file__))
png_file = os.path.sep.join(dirname.split(os.path.sep) + ['temp.png'])
s = ['110010010011', '101011010100', '110010110101', '100010010011']
s = [[int(v) for v in val] for val in s]
f = open(png_file, 'wb')
w = png.Writer(len(s[0]), len(s), greyscale=True, bitdepth=16)
w.write(f, s)
f.close()
session.upload(
view,
verbose=verbose,
thumbnail=png_file,
parallel=parallel,
workers=workers,
)
finally:
os.remove(png_file)
assert mock_post.call_count == 9
assert mock_patch.call_count == 1
assert mock_put.call_count == 1
assert mock_upload_array.call_count == 2
assert mock_upload_image.call_count == 2
mock_post.assert_has_calls(
[
mock.call(
'https://example.com/api/v1/project/myorg/myproj/files/array',
json={
'shape': [3, 3],
'dtype': 'Float64Array',
'content_type': 'application/octet-stream',
'content_length': 31,
'content_encoding': 'gzip'
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/files/array',
json={
'shape': [3],
'dtype': 'Float64Array',
'content_type': 'application/octet-stream',
'content_length':
24, # this file is 29 bytes when compressed
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/files/image',
json={
'content_type': 'image/png',
'content_length': img.seek(0, 2),
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/mappings/continuous',
json={
'gradient': 'https://example.com/api/my_colormap',
'data_controls': [0., 10., 20., 30.],
'gradient_controls': [0., 0., 1., 1.],
'visibility': [False, True, True, True, False],
'interpolate': False,
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/data/basic',
json={
'name': 'Dataset 1',
'location': 'nodes',
'array': 'https://example.com/api/self',
'mappings': [],
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/data/basic',
json={
'name':
'Dataset 2',
'description':
'Same array as dataset 1',
'location':
'nodes',
'array':
'https://example.com/api/self',
'mappings': [
'https://example.com/api/self',
'https://example.com/api/mapping_uploaded',
],
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/textures/projection',
json={
'origin': [0., 0, 0],
'axis_u': [1., 0, 0],
'axis_v': [0., 1, 0],
'image': 'https://example.com/api/self',
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/elements/pointset',
json={
'vertices':
'https://example.com/api/self',
'data': [
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
],
'defaults': {
'visible': True,
'color': {
'value': '#FF0000'
},
'opacity': {
'value': 1
},
'size': {
'value': 10
},
'shape': 'square'
},
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/views',
json={
'name':
'Test View',
'elements': [
'https://example.com/api/self',
'https://example.com/api/my_element',
],
'contents': [
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/my_colormap',
'https://example.com/api/self',
'https://example.com/api/mapping_uploaded',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/my_element',
],
},
),
],
any_order=True)
mock_patch.assert_called_with(
'https://example.com/api/mapping_uploaded',
json={
'values': ['#FF0000', '#00FF00', '#0000FF'],
'end_points': [10., 20.],
'end_inclusive': [True, True],
'visibility': [True, True, True],
},
)
mock_put.assert_called_with(
'https://example.com/api/self/thumbnail',
json={
'content_type': 'image/png',
'content_length': 88,
},
)