def test_sniffer(self):
output = 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 = load(os.path.join(
self.analysis_path, 'xdata', 'flu.json'))
output = run(
flu,
inputs={},
outputs={'data': {'type': 'table', 'format': 'rows'}}
)
self.assertEqual(output['data']['data']['fields'][:3], [
'Date', 'United States', 'Alabama'
])
def test_load_workflow(self):
flu = load(os.path.join(
self.analysis_path, 'xdata', 'flu_workflow.json'))
script_path = os.path.join(self.analysis_path, 'xdata', 'flu.py')
with open(script_path) as script_file:
script_content = script_file.read()
self.assertEqual(flu['steps'][0]['task']['script'], script_content)
def test_load_workflow(self):
flu = load(os.path.join(
self.analysis_path, 'xdata', 'flu_workflow.json'))
script_path = os.path.join(self.analysis_path, 'xdata', 'flu.py')
with open(script_path) as script_file:
script_content = script_file.read()
self.assertEqual(flu['steps'][0]['task']['script'], script_content)
def test_pgls(self):
pgls = 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')
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 = 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')
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 = load(
os.path.join(self.arbor_path, 'continuous_to_discrete.json'))
table_file = os.path.join('data', 'anolisDataAppended.csv')
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 = load(
os.path.join(self.arbor_path, 'continuous_to_discrete.json'))
table_file = os.path.join('data', 'anolisDataAppended.csv')
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_sniffer(self):
output = 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 = load(os.path.join(self.analysis_path, 'xdata', 'flu.json'))
output = run(flu,
inputs={},
outputs={'data': {
'type': 'table',
'format': 'rows'
}})
self.assertEqual(output['data']['data']['fields'][:3],
['Date', 'United States', 'Alabama'])
