def test_vector(self):
rows = {
"fields": ["a", "b"],
"rows": [
{"a": [1, 2, 3], "b": ['1', '2']},
{"a": [4, 5, 6], "b": ['3', '4']}
]
}
# Conversion to vtkTable
vtktable = girder_worker.convert(
"table",
{"format": "rows", "data": rows},
{"format": "vtktable"}
)["data"]
self.assertEqual(vtktable.GetNumberOfRows(), 2)
self.assertEqual(vtktable.GetNumberOfColumns(), 2)
a = vtktable.GetColumnByName("a")
b = vtktable.GetColumnByName("b")
self.assertEqual(a.GetNumberOfComponents(), 3)
self.assertEqual(b.GetNumberOfComponents(), 2)
self.assertTrue(isinstance(a, vtk.vtkDoubleArray))
self.assertTrue(isinstance(b, vtk.vtkStringArray))
for i in range(6):
self.assertEqual(a.GetValue(i), i + 1)
for i in range(4):
self.assertEqual(b.GetValue(i), str(i + 1))
# Conversion back to rows
rows2 = girder_worker.convert(
"table",
{"format": "vtktable", "data": vtktable},
{"format": "rows"}
)["data"]
self.assertEqual(rows2, rows)
def test_adjacencylist(self):
output = girder_worker.convert(
'graph', self.test_input['distances'], {'format': 'adjacencylist'})
expected_edges = set(self.test_input['distances']['data'].edges())
actual_edges = set()
for line in output['data'].splitlines():
parts = line.split(' ', 1)
if len(parts) > 1:
source, targets = parts
for target in targets.split(' '):
edge = (source, target)
self.assertNotIn(edge, actual_edges)
actual_edges.add(edge)
self.assertEqual(expected_edges, actual_edges)
output = girder_worker.convert(
'graph', output, {'format': 'networkx'})
# Don't take edges into consideration, because they were lost in the
# original conversion
self.assertTrue(
is_isomorphic(output['data'],
self.test_input['distances']['data'],
edge_match=None))
def test_treestore(self):
output = girder_worker.convert(
'tree',
{'format': 'newick', 'data': self.newick},
{'format': 'r.apetree'})
output = girder_worker.convert('tree', output, {'format': 'treestore'})
self.assertEqual(output['format'], 'treestore')
rows = bson.decode_all(output['data'])
for d in rows:
if 'rooted' in d:
root = d
self.assertNotEqual(root, None)
self.assertEqual(len(root['clades']), 1)
def findId(id):
for d in rows:
if d['_id'] == id:
return d
top = findId(root['clades'][0])
self.assertEqual(len(top['clades']), 2)
internal = findId(top['clades'][0])
rubribarbus = findId(top['clades'][1])
ahli = findId(internal['clades'][0])
allogus = findId(internal['clades'][1])
self.assertEqual(internal['branch_length'], 2)
self.assertEqual(ahli['name'], 'ahli')
self.assertEqual(ahli['branch_length'], 0)
self.assertEqual(allogus['name'], 'allogus')
self.assertEqual(allogus['branch_length'], 1)
self.assertEqual(rubribarbus['name'], 'rubribarbus')
self.assertEqual(rubribarbus['branch_length'], 3)
def test_treestore(self):
output = girder_worker.convert(
"tree",
{"format": "newick", "data": self.newick},
{"format": "r.apetree"})
output = girder_worker.convert("tree", output, {"format": "treestore"})
self.assertEqual(output["format"], "treestore")
rows = bson.decode_all(output["data"])
for d in rows:
if "rooted" in d:
root = d
self.assertNotEqual(root, None)
self.assertEqual(len(root["clades"]), 1)
def findId(id):
for d in rows:
if d["_id"] == id:
return d
top = findId(root["clades"][0])
self.assertEqual(len(top["clades"]), 2)
internal = findId(top["clades"][0])
rubribarbus = findId(top["clades"][1])
ahli = findId(internal["clades"][0])
allogus = findId(internal["clades"][1])
self.assertEqual(internal["branch_length"], 2)
self.assertEqual(ahli["name"], "ahli")
self.assertEqual(ahli["branch_length"], 0)
self.assertEqual(allogus["name"], "allogus")
self.assertEqual(allogus["branch_length"], 1)
self.assertEqual(rubribarbus["name"], "rubribarbus")
self.assertEqual(rubribarbus["branch_length"], 3)
def test_graphml(self):
output = girder_worker.convert(
'graph', self.test_input['distances'], {'format': 'graphml'})
expected_edges = set(self.test_input['distances']['data'].edges(
data='distance'))
actual_edges = set()
self.assertIsInstance(output['data'], (str, unicode))
tree = etree.fromstring(output['data'])
self.assertEqual(len(tree), 2)
self.assertEqual(tree[0].tag, self.GRAPHML_NS + 'key')
self.assertEqual(tree[1].tag, self.GRAPHML_NS + 'graph')
for edge in tree[1].findall(self.GRAPHML_NS + 'edge'):
edge = (edge.attrib['source'],
edge.attrib['target'],
int(edge.find(self.GRAPHML_NS + 'data').text))
self.assertNotIn(edge, actual_edges)
actual_edges.add(edge)
self.assertEqual(expected_edges, actual_edges)
output = girder_worker.convert(
'graph', output, {'format': 'networkx'})
self.assertTrue(
is_isomorphic(output['data'],
self.test_input['distances']['data'],
edge_match=numerical_edge_match('distance', 1)))
def test_non_binary_tree(self):
girder_worker.convert(
"tree",
{
"format": "newick",
"url": "file://" +
os.path.join("data", "geospiza_from_otl.phy")
},
{"format": "nested"})
def test_non_binary_tree(self):
girder_worker.convert(
'tree',
{
'format': 'newick',
'url': 'file://' +
os.path.join('data', 'geospiza_from_otl.phy')
},
{'format': 'nested'})
def test_vtkgraph(self):
# Test vtkgraph -> vtkgraph.serialized on a simple digraph
output = girder_worker.convert(
'graph', self.test_input['simpleVtkDiGraph'],
{'format': 'vtkgraph.serialized'})
with open(os.path.join(
'tests', 'data', 'vtkDiGraph.txt'), 'rb') as fixture:
self.assertEqual(output['data'].splitlines()[1:],
fixture.read().splitlines()[1:])
# Test networkx -> vtkgraph.serialized on an undirected
# graph w/ edge data
output = girder_worker.convert(
'graph', self.test_input['distances'],
{'format': 'vtkgraph.serialized'})
with open(os.path.join(
'tests', 'data', 'vtkDistancesUndirectedGraph.txt'),
'rb') as fixture:
self.assertEqual(output['data'].splitlines()[1:],
fixture.read().splitlines()[1:])
# Test networkx -> vtkgraph with missing edge attributes
output = girder_worker.convert(
'graph', self.test_input['grants'],
{'format': 'vtkgraph.serialized'})
with open(os.path.join('tests', 'data', 'vtkGrantsDirectedGraph.txt'),
'rb') as fixture:
self.assertEqual(output['data'].splitlines()[1:],
fixture.read().splitlines()[1:])
# Test networkx -> vtkgraph throws errors for different types
# of metadata
with self.assertRaises(Exception):
output = girder_worker.convert(
'graph', {'format': 'networkx', 'data': nx.Graph([
('A', 'B', {'value': 10}),
('B', 'C', {'value': '10'})
])}, {'format': 'vtkgraph'})
# Test vtkgraph -> networkx
output = girder_worker.convert(
'graph', self.test_input['simpleVtkDiGraph'],
{'format': 'networkx'})
self.assertIsInstance(output['data'], nx.DiGraph)
self.assertEqual(len(output['data'].nodes()), 3)
self.assertEqual(len(output['data'].edges()), 3)
self.assertEqual(sorted(output['data'].edges(data=True)),
[(0, 1, {'Weights': 1.0}),
(0, 2, {'Weights': 2.0}),
(1, 2, {'Weights': 1.0})])
def round_trip(self, obj):
"""Convert an object to base64 and back returning the new object."""
b64 = convert(
'python',
{'format': 'object', 'data': obj},
{'format': 'pickle.base64'}
)['data']
newobj = convert(
'python',
{'format': 'pickle.base64', 'data': b64},
{'format': 'object'}
)
return newobj['data']
def test_objectlist_to_rows(self):
objlist = [{"a": {"b": 5}}, {"a": {"b": {"c": 3}}}]
output = girder_worker.convert("table", {
"format": "objectlist",
"data": objlist
}, {"format": "rows"})
self.assertEqual(output["format"], "rows")
self.assertEqual(output["data"], {
"fields": ["a.b", "a.b.c"],
"rows": [{"a.b": 5}, {"a.b.c": 3}]})
output = girder_worker.convert("table", {
"format": "rows",
"data": output["data"]
}, {"format": "objectlist"})
self.assertEqual(output["data"], objlist)
def test_jsonlines(self):
output = girder_worker.convert("table", {
"format": "jsonlines",
"data": '{"a": 1, "b": 2}\n{"a": 3, "b": 4}'
}, {"format": "objectlist"})
self.assertEqual(output["format"], "objectlist")
self.assertEqual(output["data"], [{"a": 1, "b": 2}, {"a": 3, "b": 4}])
def test_column_names(self):
output = girder_worker.convert("table", {
"format": "rows",
"data": {"fields": ["a", "b"], "rows": [{"a": 6, "b": 5}]}
}, {"format": "column.names"})
self.assertEqual(output["format"], "column.names")
self.assertEqual(output["data"], ["a", "b"])
def test_column_names_csv(self):
output = girder_worker.convert("table", {
"format": "csv",
"data": ",a,b,longer name\n1,1,1,1\n2,2,2,2\n3,3,3,3\n"
}, {"format": "column.names"})
self.assertEqual(output["format"], "column.names")
self.assertEqual(output["data"], ["", "a", "b", "longer name"])
def test_sniffer(self):
output = girder_worker.convert(
"table",
{
"format": "csv",
"url": "file://" + os.path.join("data", "test.csv")
},
{"format": "rows"}
)
self.assertEqual(len(output["data"]["fields"]), 32)
self.assertEqual(output["data"]["fields"][:3], [
"FACILITY", "ADDRESS", "DATE OF INSPECTION"
])
self.assertEqual(len(output["data"]["rows"]), 14)
flu = girder_worker.load(os.path.join(
self.analysis_path, "xdata", "flu.json"))
output = girder_worker.run(
flu,
inputs={},
outputs={"data": {"type": "table", "format": "rows"}}
)
self.assertEqual(output["data"]["data"]["fields"][:3], [
"Date", "United States", "Alabama"
])
def test_convert(self):
tmp = tempfile.mktemp()
output = girder_worker.convert("image", {
"format": "png.base64",
"data": self.image
}, {
"format": "png",
"url": "file://" + tmp,
"mode": "auto"
})
value = open(tmp).read()
os.remove(tmp)
self.assertEqual(output["format"], "png")
self.assertEqual(base64.b64encode(value), self.image)
output = girder_worker.convert(
"image",
{"format": "png.base64", "data": self.image},
{"format": "pil"})
tmp = tempfile.mktemp()
output = girder_worker.convert(
"image",
output,
{"format": "png"})
io1 = StringIO(base64.b64decode(self.image))
im1 = Image.open(io1)
io2 = StringIO(output["data"])
im2 = Image.open(io2)
self.assertEqual(compareImages(im1, im2), 0)
output = girder_worker.convert("image", {
"format": "png.base64",
"data": self.image
}, {
"format": "jpeg"
})
data = StringIO(output['data'])
jpeg = Image.open(data)
self.assertTrue(isinstance(jpeg, JpegImageFile))
def test_convert(self):
tmp = tempfile.mktemp()
output = girder_worker.convert('image', {
'format': 'png.base64',
'data': self.image
}, {
'format': 'png',
'url': 'file://' + tmp,
'mode': 'auto'
})
value = open(tmp).read()
os.remove(tmp)
self.assertEqual(output['format'], 'png')
self.assertEqual(base64.b64encode(value), self.image)
output = girder_worker.convert(
'image',
{'format': 'png.base64', 'data': self.image},
{'format': 'pil'})
tmp = tempfile.mktemp()
output = girder_worker.convert(
'image',
output,
{'format': 'png'})
io1 = StringIO(base64.b64decode(self.image))
im1 = Image.open(io1)
io2 = StringIO(output['data'])
im2 = Image.open(io2)
self.assertEqual(compareImages(im1, im2), 0)
output = girder_worker.convert('image', {
'format': 'png.base64',
'data': self.image
}, {
'format': 'jpeg'
})
data = StringIO(output['data'])
jpeg = Image.open(data)
self.assertTrue(isinstance(jpeg, JpegImageFile))
def test_header_detection(self):
output = girder_worker.convert(
"table",
{"format": "csv", "data": "a,b,c\n7,1,c\n8,2,f\n9,3,i"},
{"format": "rows"}
)
self.assertEqual(output["data"]["fields"], ["a", "b", "c"])
self.assertEqual(len(output["data"]["rows"]), 3)
output = girder_worker.convert(
"table",
{"format": "csv", "data": "1,2,3\n7,10,\n,11,\n,12,"},
{"format": "rows"}
)
self.assertEqual(
output["data"]["fields"],
["1", "2", "3"]
)
self.assertEqual(len(output["data"]["rows"]), 3)
def test_inputs_from_file(self):
"""Run a task with base64 inputs in a file."""
a = tempfile.NamedTemporaryFile()
b = tempfile.NamedTemporaryFile()
convert(
"python", {"format": "object", "data": (0, 1)}, {"format": "pickle.base64", "mode": "local", "path": a.name}
)
convert("python", {"format": "object", "data": 2}, {"format": "pickle.base64", "mode": "local", "path": b.name})
outputs = self.run_basic_task(
{
"a": {"format": "pickle.base64", "mode": "local", "path": a.name},
"b": {"format": "pickle.base64", "mode": "local", "path": b.name},
}
)
self.assertEqual(outputs.get("c"), (0, 1, 0, 1))
self.assertEqual(outputs.get("d"), 4)
def test_clique(self):
# clique.json -> NetworkX
output = girder_worker.convert(
'graph', self.test_input['alphabetGraph'], {'format': 'networkx'})
self.assertEqual(
set([n[1]['name'] for n in output['data'].nodes(data=True)]),
set(['a', 'b', 'c', 'd']))
self.assertEqual(len(output['data'].edges()), 3)
self.assertEqual(output['data'].degree('55ba5019f8883b5bf35f3e30'), 0)
# NetworkX -> clique.json
output = girder_worker.convert(
'graph', output, {'format': 'clique.json'})
# Since the id of the nodes are lost, only test the structure
# Check nodes with names a, b, c, and d
# Check the following edges
# a -> b
# a -> c
# b -> c
output['data'] = json.loads(output['data'])
nodes = [item for item in output['data'] if item['type'] == 'node']
edges = [(item['source']['$oid'], item['target']['$oid'])
for item in output['data'] if item['type'] == 'link']
oid_by_name = {}
for node in nodes:
oid_by_name[node['data']['name']] = node['_id']['$oid']
# Check nodes
self.assertEqual(sorted(oid_by_name.keys()),
['a', 'b', 'c', 'd'])
# Check edges
self.assertEqual(len(edges), 3)
self.assertIn((oid_by_name['a'], oid_by_name['b']), edges)
self.assertIn((oid_by_name['a'], oid_by_name['c']), edges)
self.assertIn((oid_by_name['b'], oid_by_name['c']), edges)
def test_big_header(self):
output = girder_worker.convert(
"table",
{
"format": "csv",
"url": "file://" + os.path.join("data", "RadiomicsData.csv")
},
{"format": "rows"}
)
self.assertEqual(len(output["data"]["fields"]), 454)
self.assertEqual(output["data"]["fields"][:3], [
"GLCM_autocorr", "GLCM_clusProm", "GLCM_clusShade"
])
self.assertEqual(len(output["data"]["rows"]), 99)
def test_objectlist(self):
rows = {
"fields": ["a", "b"],
"rows": [
{"a": 1, "b": 'x'},
{"a": 4, "b": 'y'}
]
}
objectlist = girder_worker.convert(
"table",
{"format": "rows", "data": rows},
{"format": "objectlist"}
)["data"]
# Should have same row data
self.assertEqual(objectlist, rows["rows"])
rows2 = girder_worker.convert(
"table",
{"format": "objectlist", "data": objectlist},
{"format": "rows"}
)["data"]
# Should have same fields but could be in different order
self.assertEqual(set(rows["fields"]), set(rows2["fields"]))
# Should have same row data
self.assertEqual(rows["rows"], rows2["rows"])
# Make sure we can go back and forth to JSON
objectlist = girder_worker.convert(
"table",
girder_worker.convert(
"table",
{"format": "objectlist", "data": rows["rows"]},
{"format": "objectlist.json"}
),
{"format": "objectlist"}
)["data"]
self.assertEqual(rows["rows"], objectlist)
def test_inputs_from_file(self):
"""Run a task with base64 inputs in a file."""
a = tempfile.NamedTemporaryFile()
b = tempfile.NamedTemporaryFile()
convert(
'python',
{'format': 'object', 'data': (0, 1)},
{'format': 'pickle.base64', 'mode': 'local', 'path': a.name}
)
convert(
'python',
{'format': 'object', 'data': 2},
{'format': 'pickle.base64', 'mode': 'local', 'path': b.name}
)
outputs = self.run_basic_task({
'a': {'format': 'pickle.base64', 'mode': 'local', 'path': a.name},
'b': {'format': 'pickle.base64', 'mode': 'local', 'path': b.name}
})
self.assertEqual(outputs.get('c'), (0, 1, 0, 1))
self.assertEqual(outputs.get('d'), 4)
def test_flu(self):
output = girder_worker.convert(
"table",
{
"format": "csv",
"url": "file://" + os.path.join("data", "flu.csv")
},
{"format": "column.names"}
)
self.assertEqual(output["format"], "column.names")
self.assertEqual(len(output["data"]), 162)
self.assertEqual(
output["data"][:3],
['Date', 'United States', 'Alabama']
)
def convert(self, data_spec, format):
"""Convert to a compatible data format.
:param dict data_spec: Data specification
:param str format: The target data format
:returns: dict
>>> spec = {'name': 'a', 'type': 'number', 'format': 'number'}
>>> port = Port(spec)
>>> new_spec = port.convert({'format': 'number', 'data': 1}, 'json')
>>> new_spec['format']
'json'
>>> port.fetch(new_spec)
1
"""
return convert(self.type, data_spec, {'format': format})
def test_convert(self):
outputs = girder_worker.run(
self.cone,
inputs={
"resolution": {"format": "number", "data": 100},
"radius": {"format": "number", "data": 1}
},
outputs={
"cone": {"format": "vtkpolydata.serialized"}
})
cone = outputs["cone"]["data"]
self.assertTrue(isinstance(cone, str))
converted = girder_worker.convert(
"geometry",
outputs["cone"],
{"format": "vtkpolydata"}
)["data"]
self.assertTrue(isinstance(converted, vtk.vtkPolyData))
self.assertEqual(converted.GetNumberOfCells(), 101)
self.assertEqual(converted.GetNumberOfPoints(), 101)
def test_nan(self):
output = girder_worker.convert(
"table",
{
"format": "csv",
"url": "file://" + os.path.join("data", "RadiomicsData.csv")
},
{"format": "rows.json"}
)
data = json.loads(output["data"])
self.assertEqual(len(data["fields"]), 454)
self.assertEqual(data["fields"][:3], [
"GLCM_autocorr", "GLCM_clusProm", "GLCM_clusShade"
])
self.assertEqual(len(data["rows"]), 99)
for row in data["rows"]:
for field in row:
if isinstance(row[field], float):
self.assertFalse(math.isnan(row[field]))
self.assertFalse(math.isinf(row[field]))
def test_convert(self):
outputs = girder_worker.run(
self.cone,
inputs={
'resolution': {'format': 'number', 'data': 100},
'radius': {'format': 'number', 'data': 1}
},
outputs={
'cone': {'format': 'vtkpolydata.serialized'}
})
cone = outputs['cone']['data']
self.assertTrue(isinstance(cone, str))
converted = girder_worker.convert(
'geometry',
outputs['cone'],
{'format': 'vtkpolydata'}
)['data']
self.assertTrue(isinstance(converted, vtk.vtkPolyData))
self.assertEqual(converted.GetNumberOfCells(), 101)
self.assertEqual(converted.GetNumberOfPoints(), 101)
def run(task, inputs, outputs, task_inputs, task_outputs, validate, # noqa
auto_convert, **kwargs):
# Make map of steps
steps = {step["name"]: step for step in task["steps"]}
# Make map of input bindings
bindings = {step["name"]: {} for step in task["steps"]}
# Create dependency graph and downstream pointers
dependencies = {step["name"]: set() for step in task["steps"]}
downstream = {}
for conn in task["connections"]:
# Add dependency graph link for internal links
if "input_step" in conn and "output_step" in conn:
dependencies[conn["input_step"]].add(conn["output_step"])
# Add downstream links for links with output
if "output_step" in conn:
ds = downstream.setdefault(conn["output_step"], {})
ds_list = ds.setdefault(conn["output"], [])
ds_list.append(conn)
# Set initial bindings for inputs
if "input_step" in conn and "output_step" not in conn:
name = conn["name"]
bindings[conn["input_step"]][conn["input"]] = {
"format": task_inputs[name]["format"],
"data": inputs[name]["script_data"]
}
# Traverse analyses in topological order
for step_set in toposort(dependencies):
for step in step_set:
# Visualizations cannot be executed
if ("visualization" in steps[step] and
steps[step]["visualization"]):
continue
# Run step
print "--- beginning: %s ---" % steps[step]["name"]
out = girder_worker.run(steps[step]["task"], bindings[step])
print "--- finished: %s ---" % steps[step]["name"]
# Update bindings of downstream analyses
if step in downstream:
for name, conn_list in downstream[step].iteritems():
for conn in conn_list:
if "input_step" in conn:
# This is a connection to a downstream step
b = bindings[conn["input_step"]]
b[conn["input"]] = out[name]
else:
# This is a connection to a final output
o = outputs[conn["name"]]
o["script_data"] = out[name]["data"]
# Output visualization paramaters
outputs["_visualizations"] = []
for step in task["steps"]:
if "visualization" not in step or not step["visualization"]:
continue
vis_bindings = {}
for b, value in bindings[step["name"]].iteritems():
script_output = value
vis_input = None
for step_input in step["task"]["inputs"]:
if step_input["name"] == b:
vis_input = step_input
if not vis_input:
raise Exception(
"Could not find visualization input named " + b + "."
)
# Validate the output
if (validate and not
girder_worker.isvalid(vis_input["type"], script_output)):
raise Exception(
"Output %s (%s) is not in the expected type (%s) and "
"format (%s)." % (name, type(script_output["data"]),
vis_input["type"], script_output["format"]))
if auto_convert:
vis_bindings[b] = girder_worker.convert(
vis_input["type"],
script_output,
{"format": vis_input["format"]}
)
elif script_output["format"] == vis_input["format"]:
data = script_output["data"]
if "mode" in script_output:
girder_worker.io.push(data, script_output)
else:
vis_bindings[b] = {
"type": vis_input["type"],
"format": vis_input["format"],
"data": data
}
else:
raise Exception(
"Expected exact format match but '" +
script_output["format"] +
"' != '" + vis_input["format"] + "'."
)
if "script_data" in vis_bindings[b]:
del vis_bindings[b]["script_data"]
outputs["_visualizations"].append({
"mode": "preset",
"type": step["name"],
"inputs": vis_bindings
})
def convert(*pargs, **kwargs):
return girder_worker.convert(*pargs, **kwargs)
def run(task, inputs, outputs, task_inputs, task_outputs, validate, # noqa
auto_convert, **kwargs):
# Make map of steps
steps = {step['name']: step for step in task['steps']}
# Make map of input bindings
bindings = {step['name']: {} for step in task['steps']}
# Create dependency graph and downstream pointers
dependencies = {step['name']: set() for step in task['steps']}
downstream = {}
for conn in task['connections']:
# Add dependency graph link for internal links
if 'input_step' in conn and 'output_step' in conn:
dependencies[conn['input_step']].add(conn['output_step'])
# Add downstream links for links with output
if 'output_step' in conn:
ds = downstream.setdefault(conn['output_step'], {})
ds_list = ds.setdefault(conn['output'], [])
ds_list.append(conn)
# Set initial bindings for inputs
if 'input_step' in conn and 'output_step' not in conn:
name = conn['name']
bindings[conn['input_step']][conn['input']] = {
'format': task_inputs[name]['format'],
'data': inputs[name]['script_data']
}
# Traverse analyses in topological order
for step_set in toposort(dependencies):
for step in step_set:
# Visualizations cannot be executed
if ('visualization' in steps[step] and
steps[step]['visualization']):
continue
# Run step
print '--- beginning: %s ---' % steps[step]['name']
out = girder_worker.run(steps[step]['task'], bindings[step])
print '--- finished: %s ---' % steps[step]['name']
# Update bindings of downstream analyses
if step in downstream:
for name, conn_list in downstream[step].iteritems():
for conn in conn_list:
if 'input_step' in conn:
# This is a connection to a downstream step
b = bindings[conn['input_step']]
b[conn['input']] = out[name]
else:
# This is a connection to a final output
o = outputs[conn['name']]
o['script_data'] = out[name]['data']
# Output visualization parameters
outputs['_visualizations'] = []
for step in task['steps']:
if 'visualization' not in step or not step['visualization']:
continue
vis_bindings = {}
for b, value in bindings[step['name']].iteritems():
script_output = value
vis_input = None
for step_input in step['task']['inputs']:
if step_input['name'] == b:
vis_input = step_input
if not vis_input:
raise Exception(
'Could not find visualization input named ' + b + '.'
)
# Validate the output
if (validate and not
girder_worker.isvalid(vis_input['type'], script_output)):
raise Exception(
'Output %s (%s) is not in the expected type (%s) and '
'format (%s).' % (
name, type(script_output['data']),
vis_input['type'], script_output['format']))
if auto_convert:
vis_bindings[b] = girder_worker.convert(
vis_input['type'],
script_output,
{'format': vis_input['format']}
)
elif script_output['format'] == vis_input['format']:
data = script_output['data']
if 'mode' in script_output:
girder_worker.io.push(data, script_output)
else:
vis_bindings[b] = {
'type': vis_input['type'],
'format': vis_input['format'],
'data': data
}
else:
raise Exception(
'Expected exact format match but "' +
script_output['format'] +
'" != "' + vis_input['format'] + '".'
)
if 'script_data' in vis_bindings[b]:
del vis_bindings[b]['script_data']
outputs['_visualizations'].append({
'mode': 'preset',
'type': step['name'],
'inputs': vis_bindings
})