def test_workflow_with_generated_task_classes(self):
wf = specs.Workflow()
AddTwo = spec_class_generator("AddTwo", self.add_two)
AddThree = spec_class_generator("AddThree", self.add_three)
Multiply = spec_class_generator("Multiply", self.multiply)
wf.add_task(AddTwo(), "a2")
wf.add_task(AddThree(), "a3")
wf.add_task(Multiply(), "m")
wf.connect_tasks("a3", "m", {"b": "in1"})
wf.connect_tasks("a2", "m", {"b": "in2"})
# Add default as defined in self.workflow
wf.set_default("a3.a", {"format": "number", "data": 10})
self.assertEquals(wf, self.workflow)
inputs = {"a2.a": {"format": "json", "data": "1"},
"a3.a": {"format": "number", "data": 2}}
ground = romanesco.run(self.workflow, inputs=inputs)
system = romanesco.run(wf, inputs=inputs)
self.assertEquals(system, ground)
def test_pgls(self):
pgls = romanesco.load(os.path.join(self.arbor_path, "pgls.json"))
tree_file = os.path.join("data", "anolis.phy")
table_file = os.path.join("data", "anolisDataAppended.csv")
romanesco.run(
pgls, {
"tree": {
"format": "newick",
"url": "file://" + tree_file
},
"table": {
"format": "csv",
"url": "file://" + table_file
},
"correlation": {
"format": "text",
"data": "BM"
},
"ind_variable": {
"format": "text",
"data": "SVL"
},
"dep_variable": {
"format": "text",
"data": "PCI_limbs"
}
})
def test_workflow_with_generated_task_classes(self):
wf = specs.Workflow()
AddTwo = spec_class_generator("AddTwo", self.add_two)
AddThree = spec_class_generator("AddThree", self.add_three)
Multiply = spec_class_generator("Multiply", self.multiply)
wf.add_task(AddTwo(), "a2")
wf.add_task(AddThree(), "a3")
wf.add_task(Multiply(), "m")
wf.connect_tasks("a3", "m", {"b": "in1"})
wf.connect_tasks("a2", "m", {"b": "in2"})
# Add default as defined in self.workflow
wf.set_default("a3.a", {"format": "number", "data": 10})
self.assertEquals(wf, self.workflow)
inputs = {
"a2.a": {
"format": "json",
"data": "1"
},
"a3.a": {
"format": "number",
"data": 2
}
}
ground = romanesco.run(self.workflow, inputs=inputs)
system = romanesco.run(wf, inputs=inputs)
self.assertEquals(system, ground)
def test_chaining(self):
outputs = romanesco.run(self.analysis,
inputs={
"a": {
"format": "rows",
"data": {
"fields": ["a", "b"],
"rows": [{
"a": 1,
"b": 2
}]
}
},
"b": {
"format": "rows",
"data": {
"fields": ["a", "b"],
"rows": [{
"a": 3,
"b": 4
}]
}
}
},
outputs={"c": {
"format": "rows"
}})
outputs = romanesco.run(self.analysis,
inputs={
"a": outputs["c"],
"b": {
"format": "rows",
"data": {
"fields": ["a", "b"],
"rows": [{
"a": 5,
"b": 6
}]
}
}
},
outputs={"c": {
"format": "rows"
}})
self.assertEqual(outputs["c"]["format"], "rows")
self.assertEqual(
outputs["c"]["data"], {
"fields": ["a", "b"],
"rows": [{
"a": 1,
"b": 2
}, {
"a": 3,
"b": 4
}, {
"a": 5,
"b": 6
}]
})
def test_kwargs_debug(self):
"""Runs the table json test but with asserts for kwarg debugging"""
global _tmpfiles
romanesco.run(self.analysis, self.inputs, self.outputs, debug=True)
# Should have generated serveral files ()
self.assertGreater(len(_tmpfiles), 1)
def test_function(self):
outputs = romanesco.run(
self.function_out,
inputs={},
outputs={"output": {"format": "object"}})
self.assertEqual(outputs["output"]["data"](3)[0], 9)
outputs = romanesco.run(
self.function_in, inputs={"input": outputs["output"]})
self.assertEqual(outputs["output"]["data"], 16)
def test_function(self):
outputs = romanesco.run(self.function_out,
inputs={},
outputs={"output": {
"format": "object"
}})
self.assertEqual(outputs["output"]["data"](3)[0], 9)
outputs = romanesco.run(self.function_in,
inputs={"input": outputs["output"]})
self.assertEqual(outputs["output"]["data"], 16)
def testInlineFilepath(self):
task = {
'mode': 'python',
'script': """
fname = file
with open(file) as f:
out = f.read()
""",
'inputs': [{
'id': 'file',
'format': 'text',
'type': 'string',
'target': 'filepath'
}],
'outputs': [
{
'id': 'out',
'format': 'text',
'type': 'string'
},
{
'id': 'fname',
'format': 'text',
'type': 'string'
}
]
}
# Test filepath input
inputs = {
'file': {
'data': 'a,b,c\n1,2,3\n',
'format': 'text',
'type': 'string'
}
}
outputs = romanesco.run(task, inputs)
self.assertEqual(outputs['out']['data'], 'a,b,c\n1,2,3\n')
# Test filepath input with filename specified
task['inputs'][0]['filename'] = 'file.csv'
inputs = {
'file': {
'data': 'a,b,c\n1,2,3\n',
'format': 'text',
'type': 'string'
}
}
outputs = romanesco.run(task, inputs)
self.assertEqual(outputs['out']['data'], 'a,b,c\n1,2,3\n')
self.assertEqual(outputs['fname']['data'][-8:], 'file.csv')
def test_kwargs_debug(self):
"""Runs the table json test but with asserts for kwarg debugging"""
global _tmpfiles
romanesco.run(self.analysis,
self.inputs,
self.outputs,
write_script=True)
# Should have generated serveral files ()
self.assertGreater(len(_tmpfiles), 1)
def test_analysis_debug(self):
"""Runs the table json test but with asserts for analysis debugging"""
global _tmpfiles
romanesco.run(dict(self.analysis.items() + [("write_script", 1)]),
inputs=self.inputs,
outputs=self.outputs)
# Should have generated just one debug file
self.assertEquals(len(_tmpfiles), 1)
# File contents equals script
with open(_tmpfiles[0], "r") as fh:
self.assertEquals(fh.read(), self.script)
def test_array(self):
outputs = romanesco.run(
self.array_out,
inputs={},
outputs={"output": {"format": "serialized"}})
self.assertEqual('\n'.join(outputs["output"]["data"].split('\n')[3:]),
"131840\n14\n3\n1\n2\n3\n")
outputs = romanesco.run(
self.array_in,
inputs={"input": outputs["output"]},
outputs={"output": {"format": "serialized"}})
self.assertEqual('\n'.join(outputs["output"]["data"].split('\n')[3:]),
"131840\n14\n5\n1\n2\n3\n4\n5\n")
def test_analysis_debug(self):
"""Runs the table json test but with asserts for analysis debugging"""
global _tmpfiles
romanesco.run(dict(self.analysis.items() + [("debug", 1)]),
inputs=self.inputs,
outputs=self.outputs)
# Should have generated just one debug file
self.assertEquals(len(_tmpfiles), 1)
# File contents equals script
with open(_tmpfiles[0], "r") as fh:
self.assertEquals(fh.read(), self.script)
def test_pgls(self):
pgls = romanesco.load(os.path.join(self.arbor_path, "pgls.json"))
tree_file = os.path.join("data", "anolis.phy")
table_file = os.path.join("data", "anolisDataAppended.csv")
romanesco.run(
pgls,
{
"tree": {"format": "newick", "url": "file://" + tree_file},
"table": {"format": "csv", "url": "file://" + table_file},
"correlation": {"format": "text", "data": "BM"},
"ind_variable": {"format": "text", "data": "SVL"},
"dep_variable": {"format": "text", "data": "PCI_limbs"}
}
)
def test_cont2disc(self):
cont2disc = romanesco.load(
os.path.join(self.arbor_path, "continuous_to_discrete.json"))
table_file = os.path.join("data", "anolisDataAppended.csv")
romanesco.run(
cont2disc,
{
"table": {"format": "csv", "url": "file://" + table_file},
"column": {"format": "text", "data": "SVL"},
"thresh": {"format": "number", "data": 3.5}
},
{
"newtable": {"format": "rows"}
}
)
def testCreateZip(self):
task = {
"inputs": [{
"id": "myArchive",
"type": "directory",
"format": "zip"
}],
"outputs": [{
"id": "output",
"type": "string",
"format": "text"
}],
"script": "output = myArchive",
"mode": "python"
}
outputs = romanesco.run(task, inputs={
"myArchive": {
"format": "path",
"data": self.createFromDir
}
})
path = outputs['output']['data']
self.assertEqual(path, os.path.join(DATA_DIR, 'shapefile.zip'))
self.assertTrue(os.path.isfile(path))
with zipfile.ZipFile(path, 'r') as zf:
names = zf.namelist()
self.assertTrue('shapefile/shapefile.cpg' in names)
self.assertTrue('shapefile/shapefile.prj' in names)
def testJsonToSparkRdd(self):
analysis = {
'name': 'reduce',
'inputs': [{
'name': 'a',
'type': 'collection',
'format': 'spark.rdd'
}],
'outputs': [{
'name': 'b',
'type': 'number',
'format': 'number'
}],
'mode': 'spark.python',
'spark_conf': {
'spark.app.name': 'test_add',
'spark.master': os.environ['SPARK_TEST_MASTER_URL']
}
}
with open('data/spark_add_script.py', 'r') as fp:
script = fp.read()
analysis['script'] = script
outputs = romanesco.run(
analysis, {'a': {
'format': 'json',
'data': '[1,2,3,4,5,6,7,8,9]'
}}, {'b': {
'format': 'number'
}})
expected = {'b': {'data': 45, 'format': 'number'}}
self.assertEqual(outputs, expected)
def test_bson(self):
import pymongo
outputs = romanesco.run(self.analysis,
inputs={
"a": {
"format": "objectlist.bson",
"mode": "mongodb",
"db": "test",
"collection": "a"
},
"b": {
"format": "objectlist.bson",
"mode": "mongodb",
"db": "test",
"collection": "b"
}
},
outputs={
"c": {
"format": "objectlist.bson",
"mode": "mongodb",
"db": "test",
"collection": "temp"
}
})
self.assertEqual(outputs["c"]["format"], "objectlist.bson")
coll = pymongo.MongoClient("mongodb://localhost")["test"]["temp"]
self.assertEqual([d for d in coll.find()], [self.aobj, self.bobj])
def test_sniffer(self):
output = romanesco.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 = romanesco.load(os.path.join(
self.analysis_path, "xdata", "flu.json"))
output = romanesco.run(
flu,
inputs={},
outputs={"data": {"type": "table", "format": "rows"}}
)
self.assertEqual(output["data"]["data"]["fields"][:3], [
"Date", "United States", "Alabama"
])
def run_basic_task(self, inputs):
"""Run a basic task with pickle types."""
script = '''
c = a * b
d = b + b
'''
task = {
'inputs': [{
'name': 'a',
'type': 'python',
'format': 'object'
}, {
'name': 'b',
'type': 'python',
'format': 'object'
}],
'outputs': [{
'name': 'c',
'type': 'python',
'format': 'object'
}, {
'name': 'd',
'type': 'python',
'format': 'object'
}],
'script':
script,
'mode':
'python'
}
d = run(task, inputs=inputs, outputs={'format': 'object'})
for k, v in six.iteritems(d):
if isinstance(v, dict):
d[k] = v.get('data')
return d
def test_bson(self):
import pymongo
outputs = romanesco.run(
self.analysis,
inputs={
"a": {
"format": "objectlist.bson",
"mode": "mongodb",
"db": "test",
"collection": "a"
},
"b": {
"format": "objectlist.bson",
"mode": "mongodb",
"db": "test",
"collection": "b"
}
},
outputs={
"c": {
"format": "objectlist.bson",
"mode": "mongodb",
"db": "test",
"collection": "temp"
}
})
self.assertEqual(outputs["c"]["format"], "objectlist.bson")
coll = pymongo.MongoClient("mongodb://localhost")["test"]["temp"]
self.assertEqual([d for d in coll.find()], [self.aobj, self.bobj])
def test_r_dataframe(self):
outputs = romanesco.run(self.analysis_r,
inputs={
"a": {
"format": "rows",
"data": {
"fields": ["aa", "bb"],
"rows": [{
"aa": 1,
"bb": 2
}]
}
}
},
outputs={"b": {
"format": "rows"
}})
self.assertEqual(outputs["b"]["format"], "rows")
self.assertEqual(outputs["b"]["data"], {
"fields": ["aa", "bb"],
"rows": [{
"aa": 1,
"bb": 2
}]
})
def testDefaultInline(self):
task = {
'mode': 'python',
'script': 'b = a ** 2',
'inputs': [{
'id': 'a',
'format': 'number',
'type': 'number'
}],
'outputs': [{
'id': 'b',
'format': 'number',
'type': 'number'
}]
}
# Mode should default to "inline" if data key is set
inputs = {
'a': {
'data': 5,
'format': 'number',
'type': 'number'
}
}
outputs = romanesco.run(task, inputs)
self.assertEqual(outputs['b']['data'], 25)
def test_array(self):
outputs = romanesco.run(self.array_out,
inputs={},
outputs={"output": {
"format": "serialized"
}})
self.assertEqual('\n'.join(outputs["output"]["data"].split('\n')[3:]),
"131840\n14\n3\n1\n2\n3\n")
outputs = romanesco.run(self.array_in,
inputs={"input": outputs["output"]},
outputs={"output": {
"format": "serialized"
}})
self.assertEqual('\n'.join(outputs["output"]["data"].split('\n')[3:]),
"131840\n14\n5\n1\n2\n3\n4\n5\n")
def testCreateZip(self):
task = {
"inputs": [{
"id": "myArchive",
"type": "directory",
"format": "zip"
}],
"outputs": [{
"id": "output",
"type": "string",
"format": "text"
}],
"script": "output = myArchive",
"mode": "python"
}
outputs = romanesco.run(task,
inputs={
"myArchive": {
"format": "path",
"data": self.createFromDir
}
})
path = outputs['output']['data']
self.assertEqual(path, os.path.join(DATA_DIR, 'shapefile.zip'))
self.assertTrue(os.path.isfile(path))
with zipfile.ZipFile(path, 'r') as zf:
names = zf.namelist()
self.assertTrue('shapefile/shapefile.cpg' in names)
self.assertTrue('shapefile/shapefile.prj' in names)
def test_base64(self):
outputs = romanesco.run(
self.analysis,
inputs={
"a": {"format": "png.base64", "data": self.image},
})
self.assertEqual(outputs["pixels"]["format"], "number")
self.assertEqual(outputs["pixels"]["data"], 256)
def test_newick(self):
outputs = romanesco.run(
self.analysis,
inputs={"a": {"format": "newick", "data": self.newick}},
outputs={"b": {"format": "newick"}}
)
self.assertEqual(outputs["b"]["format"], "newick")
self.assertEqual(outputs["b"]["data"], self.newick)
def test_newick(self):
outputs = romanesco.run(
self.analysis,
inputs={"a": {"format": "newick", "data": self.newick}},
outputs={"b": {"format": "newick"}}
)
self.assertEqual(outputs["b"]["format"], "newick")
self.assertEqual(outputs["b"]["data"], self.newick)
def test_r_apetree(self):
outputs = romanesco.run(
self.analysis,
inputs={"a": {"format": "newick", "data": self.newick}},
outputs={"b": {"format": "r.apetree"}},
)
self.assertEqual(outputs["b"]["format"], "r.apetree")
self.assertEqual(str(outputs["b"]["data"])[:52], "\nPhylogenetic tree with 3 tips and 2 internal nodes.")
def test_mammal_tree(self):
mammal = romanesco.load(
os.path.join("data", "Mammal tree extraction.json"))
romanesco.run(
mammal,
{
"table": {
"format": "csv",
"url": "file://" +
os.path.join("data", "mammal_lnMass_tiny.csv")
},
"outRowCount": {"format": "number", "data": 19}
},
{
"tree": {"format": "nested"}
}
)
def test_mammal_tree(self):
mammal = romanesco.load(
os.path.join("data", "Mammal tree extraction.json"))
romanesco.run(
mammal, {
"table": {
"format":
"csv",
"url":
"file://" + os.path.join("data", "mammal_lnMass_tiny.csv")
},
"outRowCount": {
"format": "number",
"data": 19
}
}, {"tree": {
"format": "nested"
}})
def test_workflow(self):
outputs = romanesco.run(
self.workflow,
inputs={
"x": {"format": "json", "data": "1"},
"y": {"format": "number", "data": 2}
})
self.assertEqual(outputs["result"]["format"], "number")
self.assertEqual(outputs["result"]["data"], (1+3)*(2+2))
# Test using the default value for x (10).
outputs = romanesco.run(
self.workflow,
inputs={
"y": {"format": "number", "data": 2}
})
self.assertEqual(outputs["result"]["format"], "number")
self.assertEqual(outputs["result"]["data"], (10+3)*(2+2))
def test_multi_input(self):
outputs = romanesco.run(
self.multi_input,
inputs={
"x": {"format": "number", "data": 2},
"y": {"format": "number", "data": 3}
})
self.assertEqual(outputs["result"]["format"], "number")
self.assertEqual(outputs["result"]["data"], (2*2)+(3*3))
def run(*pargs, **kwargs):
jobInfo = kwargs.pop('jobInfo', {})
retval = 0
with JobManager(logPrint=jobInfo.get('logPrint', True),
url=jobInfo.get('url'), method=jobInfo.get('method'),
headers=jobInfo.get('headers')):
retval = romanesco.run(*pargs, **kwargs)
return retval
def test_workflow(self):
outputs = romanesco.run(
self.workflow,
inputs={
"x": {"format": "json", "data": "1"},
"y": {"format": "number", "data": 2}
})
self.assertEqual(outputs["result"]["format"], "number")
self.assertEqual(outputs["result"]["data"], (1+3)*(2+2))
# Test using the default value for x (10).
outputs = romanesco.run(
self.workflow,
inputs={
"y": {"format": "number", "data": 2}
})
self.assertEqual(outputs["result"]["format"], "number")
self.assertEqual(outputs["result"]["data"], (10+3)*(2+2))
def run(node=None, graph=None):
"""Computes the centrality of ``node`` (given by key) within the subgraph
represented by ``graph`` (which is in Clique-Mongo format."""
output = romanesco.run(betweenness_centrality, inputs={'G': {'format': 'clique.json',
'data': graph},
'node': {'format': 'text',
'data': node}})
return output["measure"]["data"]
def test_multi_input(self):
outputs = romanesco.run(
self.multi_input,
inputs={
"x": {"format": "number", "data": 2},
"y": {"format": "number", "data": 3}
})
self.assertEqual(outputs["result"]["format"], "number")
self.assertEqual(outputs["result"]["data"], (2*2)+(3*3))
def test_base64(self):
outputs = romanesco.run(self.analysis,
inputs={
"a": {
"format": "png.base64",
"data": self.image
},
})
self.assertEqual(outputs["pixels"]["format"], "number")
self.assertEqual(outputs["pixels"]["data"], 256)
def test_json(self):
outputs = romanesco.run(self.analysis,
inputs=self.test_input,
outputs={"c": {
"format": "rows.json"
}})
self.assertEqual(outputs["c"]["format"], "rows.json")
self.assertEqual(
outputs["c"]["data"], '{"fields": ["aa", "bb"], '
'"rows": [{"aa": 1, "bb": 2}, {"aa": 3, "bb": 4}]}')
def run(*pargs, **kwargs):
jobInfo = kwargs.pop('jobInfo', {})
retval = 0
with JobManager(logPrint=jobInfo.get('logPrint', True),
url=jobInfo.get('url'), method=jobInfo.get('method'),
headers=jobInfo.get('headers')) as jm:
kwargs['_job_manager'] = jm
retval = romanesco.run(*pargs, **kwargs)
return retval
def test_r_apetree(self):
outputs = romanesco.run(
self.analysis,
inputs={"a": {"format": "newick", "data": self.newick}},
outputs={"b": {"format": "r.apetree"}}
)
self.assertEqual(outputs["b"]["format"], "r.apetree")
self.assertEqual(
str(outputs["b"]["data"])[:52],
'\nPhylogenetic tree with 3 tips and 2 internal nodes.')
def test_r(self):
outputs = romanesco.run(
self.analysis_r,
inputs={"a": {"format": "newick", "data": self.newick}},
outputs={"b": {"format": "newick"}},
)
self.assertEqual(outputs["b"]["format"], "newick")
self.assertEqual(outputs["b"]["data"], self.newick)
outputs = romanesco.run(
self.analysis_r, inputs={"a": {"format": "nexus", "data": self.nexus}}, outputs={"b": {"format": "nexus"}}
)
self.assertEqual(outputs["b"]["format"], "nexus")
# Ignore spaces vs. tabs, and skip timestamp comment on line 2
out = "\n".join(outputs["b"]["data"].splitlines()[2:])
out = " ".join(out.split())
expected = "\n".join(self.nexus.splitlines()[2:])
expected = " ".join(expected.split())
self.assertEqual(out, expected)
def test_json(self):
outputs = romanesco.run(
self.analysis,
inputs={
"a": {"format": "json", "data": '"hi, "'},
"b": {"format": "json", "data": '"there"'}
},
outputs={
"c": {"format": "json"}
})
self.assertEqual(outputs["c"]["format"], "json")
self.assertEqual(outputs["c"]["data"], '"hi, there"')
def test_text(self):
outputs = romanesco.run(
self.analysis,
inputs={
"a": {"format": "text", "data": "hi, "},
"b": {"format": "text", "data": "there"}
},
outputs={
"c": {"format": "text"}
})
self.assertEqual(outputs["c"]["format"], "text")
self.assertEqual(outputs["c"]["data"], "hi, there")
def test_cont2disc(self):
cont2disc = romanesco.load(
os.path.join(self.arbor_path, "continuous_to_discrete.json"))
table_file = os.path.join("data", "anolisDataAppended.csv")
romanesco.run(
cont2disc, {
"table": {
"format": "csv",
"url": "file://" + table_file
},
"column": {
"format": "text",
"data": "SVL"
},
"thresh": {
"format": "number",
"data": 3.5
}
}, {"newtable": {
"format": "rows"
}})
def test_json(self):
outputs = romanesco.run(
self.analysis,
inputs=self.test_input,
outputs={
"c": {"format": "rows.json"}
})
self.assertEqual(outputs["c"]["format"], "rows.json")
self.assertEqual(
outputs["c"]["data"],
'{"fields": ["aa", "bb"], '
'"rows": [{"aa": 1, "bb": 2}, {"aa": 3, "bb": 4}]}')
def test_float(self):
outputs = romanesco.run(
self.analysis,
inputs={
"a": {"format": "number", "data": 1.5},
"b": {"format": "number", "data": 2.5}
},
outputs={
"c": {"format": "number"}
})
self.assertEqual(outputs["c"]["format"], "number")
self.assertEqual(outputs["c"]["data"], 4)
def testContourAnalysis(self):
"""
Test contour analysis
"""
inputs = {
'host': {
'format': 'json',
'data': 'localhost'
},
'port': {
'format': 'json',
'data': girder_port
},
'token': {
'format': 'json',
'data': self._client.token
},
'fileId': {
'format': 'json',
'data': self._dataset_file_id
},
'variable': {
'format': 'json',
'data': 'pr'
},
'timestep': {
'format': 'number',
'data': 0
}
}
outputs = {
'result': {
'format': 'json'
}
}
analysis = self._analysis['meta']['analysis']
result = romanesco.run(analysis, inputs=inputs, outputs=outputs)
output_item_id = str(result['output_item_id']['data'])
# Download the item and check it what we expect
path = '/item/%s/download' % output_item_id
response = self.request(path=path, method='GET', user=self._user)
self.assertStatusOk(response)
data_path = os.path.join(os.path.dirname(__file__), 'data', 'expected_contour.json' )
with open(data_path, 'r') as fp:
expected_result = json.load(fp)
self.assertEquals(response.json, expected_result, 'Unexpected result')
def test_cone(self):
outputs = romanesco.run(
self.cone,
inputs={
"resolution": {"format": "number", "data": 100},
"radius": {"format": "number", "data": 1}
})
self.assertEqual(outputs["cone"]["format"], "vtkpolydata")
cone = outputs["cone"]["data"]
self.assertTrue(isinstance(cone, vtk.vtkPolyData))
self.assertEqual(cone.GetNumberOfCells(), 101)
self.assertEqual(cone.GetNumberOfPoints(), 101)
def test_json(self):
outputs = romanesco.run(
self.analysis,
inputs={
"a": {"format": "json", "data": "1"},
"b": {"format": "json", "data": "2"}
},
outputs={
"c": {"format": "json"}
})
self.assertEqual(outputs["c"]["format"], "json")
self.assertEqual(outputs["c"]["data"], "3")
def testMagicVariables(self):
task = {
'outputs': [{
'id': '_tempdir',
'type': 'string',
'format': 'text'
}],
'script': ''
}
outputs = romanesco.run(task)
self.assertTrue('_tempdir' in outputs)
self.assertRegexpMatches(outputs['_tempdir']['data'], _tmp + '.+')
def test_r(self):
outputs = romanesco.run(
self.analysis_r,
inputs={"a": {"format": "newick", "data": self.newick}},
outputs={"b": {"format": "newick"}}
)
self.assertEqual(outputs["b"]["format"], "newick")
self.assertEqual(outputs["b"]["data"], self.newick)
outputs = romanesco.run(
self.analysis_r,
inputs={"a": {"format": "nexus", "data": self.nexus}},
outputs={"b": {"format": "nexus"}}
)
self.assertEqual(outputs["b"]["format"], "nexus")
# Ignore spaces vs. tabs, and skip timestamp comment on line 2
out = "\n".join(outputs["b"]["data"].splitlines()[2:])
out = " ".join(out.split())
expected = "\n".join(self.nexus.splitlines()[2:])
expected = " ".join(expected.split())
self.assertEqual(out, expected)
def test_tsv(self):
outputs = romanesco.run(
self.analysis,
inputs={
"a": {"format": "csv", "data": 'a,b,c\n1,2,3'},
"b": {"format": "tsv", "data": 'a\tb\tc\n4\t5\t6'}
},
outputs={
"c": {"format": "tsv"}
})
self.assertEqual(outputs["c"]["format"], "tsv")
self.assertEqual(outputs["c"]["data"].splitlines(),
["a\tb\tc", "1\t2\t3", "4\t5\t6"])
def test_unicode(self):
outputs = romanesco.run(
self.analysis,
inputs={
"a": {"format": "text", "data": u"hi, "},
"b": {"format": "text", "data": u"there"}
},
outputs={
"c": {"format": "text"}
})
self.assertEqual(outputs["c"]["format"], "text")
self.assertEqual(outputs["c"]["data"], u"hi, there")
self.assertIsInstance(outputs["c"]["data"], unicode)
def test_vtktable(self):
outputs = romanesco.run(self.analysis,
inputs=self.test_input,
outputs={"c": {
"format": "vtktable"
}})
self.assertEqual(outputs["c"]["format"], "vtktable")
t = outputs["c"]["data"]
self.assertEqual(t.GetNumberOfRows(), 2)
self.assertEqual(t.GetNumberOfColumns(), 2)
self.assertEqual(t.GetValueByName(0, "aa"), 1)
self.assertEqual(t.GetValueByName(1, "aa"), 3)
self.assertEqual(t.GetValueByName(0, "bb"), 2)
self.assertEqual(t.GetValueByName(1, "bb"), 4)
def test_file(self):
tmp = tempfile.mktemp()
outputs = romanesco.run(
self.analysis,
inputs=self.test_input,
outputs={"c": {
"format": "csv",
"path": tmp,
"mode": "local"
}})
with open(tmp, 'r') as fp:
output = fp.read()
os.remove(tmp)
self.assertEqual(outputs["c"]["format"], "csv")
self.assertEqual(output.splitlines(), ["aa,bb", "1,2", "3,4"])
def testExtractTgz(self):
outputs = romanesco.run(
self.extractTask,
inputs={"myDir": {
"format": "tgz",
"data": self.tarFile
}})
self.assertEqual(set(outputs['files']['data']),
set(('provision.retry', 'site.retry')))
self.assertEqual(outputs['myDir']['data'], self.tarDir)
self.assertTrue(os.path.isdir(self.tarDir))
self.assertTrue(os.path.isfile(os.path.join(self.tarDir,
'site.retry')))
self.assertTrue(
os.path.isfile(os.path.join(self.tarDir, 'provision.retry')))
def test_json(self):
outputs = romanesco.run(self.analysis,
inputs={
"a": {
"format": "json",
"data": '"hi, "'
},
"b": {
"format": "json",
"data": '"there"'
}
},
outputs={"c": {
"format": "json"
}})
self.assertEqual(outputs["c"]["format"], "json")
self.assertEqual(outputs["c"]["data"], '"hi, there"')
def test_json(self):
outputs = romanesco.run(self.analysis,
inputs={
"a": {
"format": "json",
"data": "1"
},
"b": {
"format": "json",
"data": "2"
}
},
outputs={"c": {
"format": "json"
}})
self.assertEqual(outputs["c"]["format"], "json")
self.assertEqual(outputs["c"]["data"], "3")
def test_float(self):
outputs = romanesco.run(self.analysis,
inputs={
"a": {
"format": "number",
"data": 1.5
},
"b": {
"format": "number",
"data": 2.5
}
},
outputs={"c": {
"format": "number"
}})
self.assertEqual(outputs["c"]["format"], "number")
self.assertEqual(outputs["c"]["data"], 4)
def test_cone(self):
outputs = romanesco.run(self.cone,
inputs={
"resolution": {
"format": "number",
"data": 100
},
"radius": {
"format": "number",
"data": 1
}
})
self.assertEqual(outputs["cone"]["format"], "vtkpolydata")
cone = outputs["cone"]["data"]
self.assertTrue(isinstance(cone, vtk.vtkPolyData))
self.assertEqual(cone.GetNumberOfCells(), 101)
self.assertEqual(cone.GetNumberOfPoints(), 101)
