def test_protocol_parameters():
res = protocol_parser.parse(os.path.join(data_path, 'test_parameters.py'))
expected_parameters = [
{
"name": "a",
"annotation": {'type': 'int'},
"default": 12
},
{
"name": "b",
"annotation": None,
"default": "woo"
},
{
"name": "plate_type",
"annotation": {
"type": "StringSelection",
"options": [
{"value": "96-flat", "text": "96 flat"},
{"value": "96-PCR-flat", "text": "96 PCR flat"},
{"value": "96-PCR-tall", "text": "96 PCR tall"}
]},
"default": '96-flat'
}
]
assert res["parameters"] == expected_parameters
def test_protocol_parse():
res = protocol_parser.parse(os.path.join(data_path, 'test.py'))
expected = {
'containers': [
{
'name': "tiprack-10ul",
'type': "tiprack-10ul",
'slot': "C2"
},
{
'name': "tiprack-200ul",
'type': "tiprack-200ul",
'slot': "A1"
},
{
'name': "trough",
'type': "trough-12row",
'slot': "E1"
},
{
'name': "plate",
'type': "96-PCR-flat",
'slot': "C1"
},
{
'name': "trash",
'type': "point",
'slot': "B2"
}
],
'instruments': [
{
'name': 'p200',
'type': 'pipette',
'channels': 8,
'axis': 'a',
'max_volume': 200,
'min_volume': 20
},
{
'name': 'p10',
'type': 'pipette',
'channels': 1,
'axis': 'b',
'max_volume': 10,
'min_volume': 1
}
],
'parameters': []
}
assert res == expected
def scan(root):
"""
Recursively scan through root returning the list of protocol
dictionary items.
"""
protocols = [
{
**protocol,
**protocol_parser.parse(get_protocol_pyfile(protocol)),
**markdown_parser.parse(get_protocol_mdfile(protocol))
} for protocol in get_valid_protocols(root)
if protocol['status'] != 'empty' and
# Skipping root dir
protocol['slug'] != '.' and not protocol['flags']['ignore']
]
return protocols