def test_quick_wire_to_input_array_with_set_sample(session):
canvas = Planner(session)
frags = session.Sample.where(
{"sample_type_id": session.SampleType.find_by_name("Fragment").id},
opts={"limit": 10},
)
purify1 = canvas.create_operation_by_name("Purify Gel Slice", category="Cloning")
purify2 = canvas.create_operation_by_name("Purify Gel Slice", category="Cloning")
canvas.set_field_value(purify1.inputs[0], sample=frags[0])
canvas.set_field_value(purify2.inputs[0], sample=frags[1])
assemble = canvas.create_operation_by_name("Assemble Plasmid", category="Cloning")
canvas.quick_wire(purify1, assemble)
canvas.quick_wire(purify2, assemble)
canvas.chain("Purify Gel Slice", assemble, category="Cloning")
input_array = assemble.input_array("Fragment")
assert len(input_array) == 3, "There should be 3 field values"
assert input_array[0].sample == frags[0]
assert input_array[1].sample == frags[1]
assert input_array[2].sample is None
def test_optimize_case2(self, session):
"""Here, we are trying to optimize two chains of 5 operations.
We expect to merge 10 operation to 5 operations.
"""
with session.with_cache() as sess:
canvas = Planner(sess)
q = self.sql({
"object_type_id":
sess.ObjectType.find_by_name("E coli Plate of Plasmid").id,
"location":
self.Not("deleted"),
})
item = sess.Item.one(query=q)
assert item
chain = [
"Check Plate",
"Make Overnight Suspension",
"Make Miniprep",
"Yeast Transformation",
"Yeast Overnight Suspension",
]
yeasts = session.Sample.last(
2,
query={
"sample_type_id":
session.SampleType.find_by_name("Yeast Strain").id
},
)
for i in range(2):
ops = canvas.chain(*chain)
canvas.set_field_value_and_propogate(ops[0].inputs[0],
sample=item.sample)
canvas.set_to_available_item(ops[0].inputs[0])
canvas.set_field_value_and_propogate(ops[-1].outputs[0],
sample=yeasts[0])
canvas.set_field_value(ops[-2].inputs[1], sample=yeasts[1])
assert len(canvas.plan.operations) == 10
canvas.optimize()
# we expect to merge everything except 'Yeast Transformation' and
# 'Yeast Overnight' since these have absent sample definition for either
# their input or outputs and FieldValues with no samples are never mergable.
expected_op_types = [
"Check Plate",
"Make Miniprep",
"Make Overnight Suspension",
"Yeast Overnight Suspension",
"Yeast Transformation",
]
op_types = sorted(
[op.operation_type.name for op in canvas.operations])
assert len(canvas.plan.operations) == 5
assert expected_op_types == op_types
def test_inventory_updater(session):
ot = session.ObjectType.one(query="rows > 2 AND columns > 2")
collection = session.Collection.new(object_type=ot)
primer = session.SampleType.find_by_name("Primer")
fragment = session.SampleType.find_by_name("Fragment")
plasmid = session.SampleType.find_by_name("Plasmid")
yeast = session.SampleType.find_by_name("Yeast Strain")
frag = fragment.new_sample(
str(uuid4()),
project="test",
description="",
properties={
"Forward Primer":
primer.new_sample(
str(uuid4()),
project="test",
description="",
properties={
"Anneal Sequence": "AGGGATAT",
"T Anneal": 50
},
),
"Length":
1000,
"Sequence":
"",
},
)
collection[0, 0] = frag
item = session.Item.new(
object_type=session.ObjectType.find_by_name("Fragment Stock"),
sample=collection.sample_matrix[0, 0],
)
print(item.object_type)
planner = Planner(session)
op = planner.create_operation_by_name("Make PCR Fragment")
planner.set_field_value(op.input("Template"), item=item)
saved = save_inventory(session, [planner.plan, collection])
# assert frag in saved
assert frag.id
assert frag.properties["Forward Primer"].id
assert item.id
assert planner.plan.id
assert collection.id
save_inventory(session, [planner.plan, collection], merge_samples=True)
def test_add_wire_sets_sample_from_source(session):
session.set_verbose(True)
canvas = Planner(session)
assert len(canvas.plan.wires) == 0
p = session.Sample.one(
query=dict(sample_type_id=session.SampleType.find_by_name("Primer").id)
)
destination = canvas.create_operation_by_name(
"Make PCR Fragment", category="Cloning"
)
source = canvas.create_operation_by_name("Rehydrate Primer", category="Cloning")
canvas.set_field_value(source.outputs[0], sample=p)
canvas.add_wire(source.outputs[0], destination.input("Forward Primer"))
assert destination.input("Forward Primer").sample.id == p.id
def test_optimize_case3_array_inputs(self, session):
"""Here we test whether operation types with field_value array inputs
are mergable despite being in a different order."""
with session.with_cache() as sess:
canvas = Planner(sess)
q = self.sql({
"object_type_id":
sess.ObjectType.find_by_name("Fragment Stock").id,
"location":
self.Not("deleted"),
})
items = sess.Item.last(4, query=q)
assert items
assemble_op1 = canvas.create_operation_by_name("Assemble Plasmid")
assemble_op2 = canvas.create_operation_by_name("Assemble Plasmid")
assemble_op3 = canvas.create_operation_by_name("Assemble Plasmid")
assemble_op4 = canvas.create_operation_by_name("Assemble Plasmid")
assemble_op1.add_to_input_array("Fragment", item=items[0])
assemble_op1.add_to_input_array("Fragment", item=items[1])
assemble_op2.add_to_input_array("Fragment", item=items[0])
assemble_op2.add_to_input_array("Fragment", item=items[1])
assemble_op3.add_to_input_array("Fragment", item=items[1])
assemble_op3.add_to_input_array("Fragment", item=items[0])
assemble_op4.add_to_input_array("Fragment", item=items[1])
assemble_op4.add_to_input_array("Fragment", item=items[2])
sample = sess.Sample.one(query={
"sample_type_id":
sess.SampleType.find_by_name("Plasmid").id
})
canvas.set_field_value(assemble_op1.outputs[0], sample=sample)
canvas.set_field_value(assemble_op2.outputs[0], sample=sample)
canvas.set_field_value(assemble_op3.outputs[0], sample=sample)
canvas.set_field_value(assemble_op4.outputs[0], sample=sample)
assert len(canvas.plan.operations) == 4
canvas.optimize()
assert len(canvas.plan.operations) == 2
def test_restrict_to_one(self, session, restrict_to_one):
with session.with_cache() as sess:
sess.set_verbose(True)
p = Planner(sess)
for i in range(2):
comp_cell_type = session.ObjectType.find_by_name(
"Yeast Competent Cell")
comp_cells = session.Item.last(
100,
query='object_type_id = {} AND location != "deleted"'.
format(comp_cell_type.id),
)
grouped_by_samples = {}
for c in comp_cells:
grouped_by_samples.setdefault(c.sample_id,
list()).append(c)
more_than_one = [
cells for cells in grouped_by_samples.values()
if len(cells) > 1
][0]
assert more_than_one
parent_sample = more_than_one[0].sample
op = p.create_operation_by_name("Yeast Transformation")
p.set_field_value(op.input("Parent"), sample=parent_sample)
if restrict_to_one:
p.set_to_available_item(
op.input("Parent"),
item_preference=p.ITEM_SELECTION_PREFERENCE.
RESTRICT_TO_ONE,
)
else:
p.set_to_available_item(op.input("Parent"))
items = set()
for op in p.plan.operations:
for fv in op.field_values:
if fv.child_item_id:
items.add(fv.child_item_id)
if restrict_to_one:
assert len(items) == 2
else:
assert len(items) == 1
def test_proper_setting_of_object_types(session):
canvas = Planner(session)
yeast = session.Sample.where(
{"sample_type_id": session.SampleType.find_by_name("Yeast Strain").id},
opts={"limit": 10},
)[-1]
streak = canvas.create_operation_by_name("Streak Plate", category="Yeast")
glycerol = canvas.create_operation_by_name("Yeast Glycerol Stock", category="Yeast")
canvas.set_field_value(glycerol.inputs[0], sample=yeast)
canvas.set_field_value(streak.inputs[0], sample=yeast)
mating = canvas.create_operation_by_name("Yeast Mating")
canvas.add_wire(streak.outputs[0], mating.inputs[0])
canvas.add_wire(glycerol.outputs[0], mating.inputs[1])
assert (
mating.inputs[0].allowable_field_type.object_type.name == "Divided Yeast Plate"
)
assert (
mating.inputs[1].allowable_field_type.object_type.name == "Yeast Glycerol Stock"
)
def test_optimize_case5_array_inputs_merge_missing_samples(self, session):
with session.with_cache() as sess:
canvas = Planner(sess)
canvas.logger.set_level("DEBUG")
q = self.sql({
"object_type_id":
sess.ObjectType.find_by_name("Fragment Stock").id,
"location":
self.Not("deleted"),
})
primers = sess.Sample.last(
4,
query={
"sample_type_id": sess.SampleType.find_by_name("Primer").id
})
fragments = sess.Sample.last(
4,
query={
"sample_type_id":
sess.SampleType.find_by_name("Fragment").id
})
plasmids = sess.Sample.last(
3,
query={
"sample_type_id":
sess.SampleType.find_by_name("Plasmid").id
})
subchain = [
"Make PCR Fragment",
"Run Gel",
"Extract Gel Slice",
"Purify Gel Slice",
]
ops1 = canvas.chain(*(subchain + ["Assemble Plasmid"]))
ops2 = canvas.chain(*(subchain + ops1[-1:]))
ops3 = canvas.chain(*(subchain + ["Assemble Plasmid"]))
ops4 = canvas.chain(*(subchain + ops3[-1:]))
ops5 = canvas.chain(*(subchain + ["Assemble Plasmid"]))
ops6 = canvas.chain(*(subchain + ops5[-1:]))
ops7 = canvas.chain(*(subchain + ops5[-1:]))
ops8 = canvas.chain(*(subchain + ops5[-1:]))
ops9 = canvas.chain(*(subchain + ops5[-1:]))
for op in canvas.get_op_by_name("Run Gel"):
pour_gel = canvas.chain("Pour Gel", op)[0]
# pour_gels = [op for op in canvas.operations if
# op.operation_type.name == 'Pour Gel']
# print([op.outputs[0].sample for op in pour_gels])
# chain1 using primer1
canvas.set_field_value_and_propogate(ops1[0].outputs[0],
sample=fragments[0])
# chain2 using primer2
canvas.set_field_value_and_propogate(ops2[0].outputs[0],
sample=fragments[1])
# chain3 using primer2
canvas.set_field_value_and_propogate(ops3[0].outputs[0],
sample=fragments[1])
# chain4 using primer1
canvas.set_field_value_and_propogate(ops4[0].outputs[0],
sample=fragments[0])
canvas.set_field_value_and_propogate(ops6[0].outputs[0],
sample=fragments[1])
canvas.set_field_value_and_propogate(ops7[0].outputs[0],
sample=fragments[1])
def pcr(op, p1, p2, t):
canvas.set_field_value(op.input("Forward Primer"), sample=p1)
canvas.set_field_value(op.input("Reverse Primer"), sample=p2)
canvas.set_field_value(op.input("Template"), sample=t)
pcr(ops1[0], primers[0], primers[1], plasmids[0])
pcr(ops2[0], primers[2], primers[3], plasmids[1])
pcr(ops4[0], primers[0], primers[1], plasmids[0])
pcr(ops3[0], primers[2], primers[3], plasmids[1])
canvas.set_field_value(ops1[-1].outputs[0], sample=plasmids[2])
canvas.set_field_value(ops3[-1].outputs[0], sample=plasmids[2])
op_types = sorted(
[op.operation_type.name for op in canvas.operations])
print(op_types)
canvas.optimize(merge_missing_samples=True)
op_types = sorted(
[op.operation_type.name for op in canvas.operations])
print(op_types)
assert len(canvas.get_op_by_name("Assemble Plasmid")) == 2
assert len(canvas.get_op_by_name("Pour Gel")) == 4
for op in canvas.get_op_by_name("Assemble Plasmid"):
assert len({fv.child_sample_id for fv in op.inputs}) == 2
assert len(op.inputs) in [5, 2]
