/
AP2En_test.py
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/
AP2En_test.py
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import json
import unittest
import pytest
from transcriptic import english
class AP2EnTestCase(unittest.TestCase):
def test_web_example(self):
with open("./test/resources/web_example.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
forest, [[1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]]
)
def test_med_json_job_tree(self):
pjsonString = """{
"refs": {
"3-384-pcr": {
"new": "384-pcr",
"discard": true
},
"5-384-pcr": {
"new": "384-pcr",
"discard": true
},
"4-384-pcr": {
"new": "384-pcr",
"discard": true
},
"1-384-pcr": {
"new": "384-pcr",
"discard": true
},
"0-384-pcr": {
"new": "384-pcr",
"discard": true
},
"6-384-pcr": {
"new": "384-pcr",
"discard": true
},
"2-384-pcr": {
"new": "384-pcr",
"discard": true
}
},
"instructions": [
{
"groups": [
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "3-384-pcr/383",
"from": "3-384-pcr/0"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "3-384-pcr/382",
"from": "3-384-pcr/1"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "5-384-pcr/383",
"from": "5-384-pcr/0"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "5-384-pcr/382",
"from": "5-384-pcr/1"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "4-384-pcr/383",
"from": "4-384-pcr/0"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "4-384-pcr/382",
"from": "4-384-pcr/1"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "1-384-pcr/383",
"from": "1-384-pcr/0"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "1-384-pcr/382",
"from": "1-384-pcr/1"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "0-384-pcr/383",
"from": "0-384-pcr/0"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "0-384-pcr/382",
"from": "0-384-pcr/1"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "6-384-pcr/383",
"from": "6-384-pcr/0"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "6-384-pcr/382",
"from": "6-384-pcr/1"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "2-384-pcr/383",
"from": "2-384-pcr/0"
}
],
"x_tip_type": "filtered50"
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "2-384-pcr/382",
"from": "2-384-pcr/1"
}
],
"x_tip_type": "filtered50"
}
],
"op": "pipette"
}
]
}
"""
pjson = json.loads(pjsonString)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
forest,
[[1, [2]], [3, [4]], [5, [6]], [7, [8]], [9, [10]], [11, [12]], [13, [14]]],
)
def test_measure_suite(self):
"""
Desired Output:
1. Measure concentration of 2.0 microliters DNA source aliquots
2. Measure mass of test_plate2
3. Measure volume of 12 wells from test_plate
4. Measure volume of 8 wells from test_plate2
"""
with open("./test/resources/measure_suite.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Measure concentration of 2.0 microliters DNA source aliquots of test_plate2",
"Measure mass of test_plate2",
"Measure volume of 12 wells from test_plate",
"Measure volume of 8 wells from test_plate2",
],
)
self.assertEqual(forest, [[1, [2, [4]]], [3]])
def test_mag_incubate(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically incubate pcr_0 for 30.0 minutes with a tip position of 1.5
"""
with open("./test/resources/mag_incubate.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically incubate pcr_0 for 30.0 minutes with a tip position of 1.5",
],
)
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
def test_mag_mix(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically mix pcr_0 beads for 30.0 seconds at an amplitude of 0
"""
with open("./test/resources/mag_mix.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically mix pcr_0 beads for 30.0 seconds at an amplitude of 0",
],
)
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
def test_mag_dry(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically dry pcr_0 for 30.0 minutes
"""
with open("./test/resources/mag_dry.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically dry pcr_0 for 30.0 minutes",
],
)
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
def test_mag_collect(self):
"""
Desired Output:
1. Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0
2. Distribute from test/1 into wells test/7, test/8, test/9
3. Distribute from test/2 into wells test/10
4. Distribute from test/0 into wells test/1
5. Magnetically collect pcr_0 beads for 5 cycles with a pause duration of 30.0 seconds
"""
with open("./test/resources/mag_collect.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Magnetically release pcr_0 beads for 30.0 seconds at an amplitude of 0",
"Distribute from test/1 into wells test/7, test/8, test/9",
"Distribute from test/2 into wells test/10",
"Distribute from test/0 into wells test/1",
"Magnetically collect pcr_0 beads for 5 cycles with a pause duration of 30.0 seconds",
],
)
self.assertEqual(forest, [[1, [5]], [2, [4]], [3]])
def test_purify(self):
"""
Desired Output:
1. Perform gel purification on the 0.8% agarose gel with band range(s) 0-10
2. Perform gel purification on the 0.8% agarose gel with band range(s) 0-10
3. Perform gel purification on the 0.8% agarose gel with band range(s) 0-10
"""
with open("./test/resources/purify.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Perform gel purification on the 0.8% agarose gel with band range(s) 0-10",
"Perform gel purification on the 0.8% agarose gel with band range(s) 0-10",
"Perform gel purification on the 0.8% agarose gel with band range(s) 0-10",
],
)
self.assertEqual(forest, [[1, [2, [3]]]])
def test_dispense_suite(self):
"""
Desired Output:
1. Dispense 100 microliters of water to the full plate of sample_plate5
2. Dispense corresponding amounts of water to 12 column(s) of sample_plate5
3. Dispense 50 microliters of reagent with resource ID rs17gmh5wafm5p to the full plate of sample_plate5
"""
with open("./test/resources/dispense.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Dispense 100 microliters of water to the full plate of sample_plate5",
"Dispense corresponding amounts of water to 12 column(s) of sample_plate5",
"Dispense 50 microliters of resource with resource ID rs17gmh5wafm5p to the full plate of sample_plate5",
],
)
self.assertEqual(forest, [[1, [2, [3]]]])
def test_illumina(self):
"""
Desired Output:
1. Illumina sequence wells test_plate6/0, test_plate6/1 with library size 34
"""
with open("./test/resources/illumina.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Illumina sequence wells test_plate6/0, test_plate6/1 with library size 34"
],
)
self.assertEqual(forest, [[1]])
def test_flow(self):
"""
Desired Output:
1. Perform flow cytometry on well0 with the respective FSC and SSC channel parameters
"""
with open("./test/resources/flow.json") as data_file:
pjson = json.load(data_file)
parser_instance = english.AutoprotocolParser(pjson)
parser_instance.job_tree()
parsed_output = parser_instance.parsed_output
steps = parser_instance.object_list
forest = parser_instance.forest_list
self.assertEqual(
parsed_output,
[
"Perform flow cytometry on test_plate/0 with the respective FSC and SSC channel parameters"
],
)
self.assertEqual(forest, [[1]])