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_pgls(self):
pgls = girder_worker.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')
girder_worker.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_pgls(self):
pgls = girder_worker.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")
girder_worker.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 = girder_worker.load(
os.path.join(self.arbor_path, 'continuous_to_discrete.json'))
table_file = os.path.join('data', 'anolisDataAppended.csv')
girder_worker.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_cont2disc(self):
cont2disc = girder_worker.load(
os.path.join(self.arbor_path, "continuous_to_discrete.json"))
table_file = os.path.join("data", "anolisDataAppended.csv")
girder_worker.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_mammal_tree(self):
mammal = girder_worker.load(
os.path.join("data", "Mammal tree extraction.json"))
girder_worker.run(
mammal,
{
"table": {
"format": "csv",
"url": "file://" +
os.path.join("data", "mammal_lnMass_tiny.csv")
},
"outRowCount": {"format": "number", "data": 19}
},
{
"tree": {"format": "nested"}
}
)