def test_raises_exception_wiring_with_no_afts(session):
canvas = Planner(session)
op1 = canvas.create_operation_by_name("Make PCR Fragment", category="Cloning")
op2 = canvas.create_operation_by_name("Check Plate", category="Cloning")
with pytest.raises(PlannerException):
canvas._set_wire(op1.outputs[0], op2.inputs[0])
def test_collect_matching_afts(session):
canvas = Planner(session)
op1 = canvas.create_operation_by_name("Check Plate", category="Cloning")
op2 = canvas.create_operation_by_name("E Coli Lysate", category="Cloning")
afts = canvas._collect_matching_afts(op1, op2)
print(afts)
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_prettify(session):
with session.with_cache() as sess:
canvas = Planner(sess)
for i in range(10):
canvas.create_operation_by_name("Yeast Overnight Suspension")
canvas.prettify()
def test_canvas_add_op(session):
canvas = Planner(session)
canvas.create_operation_by_name("Yeast Transformation")
canvas.create_operation_by_name("Yeast Antibiotic Plating")
canvas.quick_wire_by_name("Yeast Transformation", "Yeast Antibiotic Plating")
canvas.create()
p = session.Plan.find(canvas.plan.id)
pass
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_set_input_array(session):
canvas = Planner(session)
op = canvas.create_operation_by_name("Assemble Plasmid", category="Cloning")
frags = session.Sample.where(
{"sample_type_id": session.SampleType.find_by_name("Fragment").id},
opts={"limit": 10},
)
canvas.set_input_field_value_array(op, "Fragment", sample=frags[0])
canvas.set_input_field_value_array(op, "Fragment", sample=frags[1])
input_array = op.input_array("Fragment")
assert (
len(op.input_array("Fragment")) == 2
), "There should be exactly 2 field values in the input array"
assert (
input_array[0] != input_array[1]
), "Input array field values should be different"
assert len(op.input_array("Fragment")) == 2
assert (
op.input_array("Fragment")[0].sample == frags[0]
), "Input array 0 should have fragment 0"
assert (
op.input_array("Fragment")[1].sample == frags[1]
), "Input array 1 should have fragment 1"
def test_quick_chain_to_existing_operation_too_many_times(session):
canvas = Planner(session)
op = canvas.create_operation_by_name("Yeast Transformation")
op1 = canvas.chain(op, "Check Yeast Plate")[-1]
with pytest.raises(PlannerException):
canvas.chain("Yeast Transformation", op1)
assert len(canvas.plan.wires) == 1
def test_add_wire(session):
canvas = Planner(session)
assert len(canvas.plan.wires) == 0
op1 = canvas.create_operation_by_name("Make PCR Fragment", category="Cloning")
op2 = canvas.create_operation_by_name("Rehydrate Primer", category="Cloning")
canvas.add_wire(op2.outputs[0], op1.input("Forward Primer"))
assert len(canvas.plan.wires) == 1
wire = canvas.plan.wires[0]
assert (
wire.source.allowable_field_type.sample_type_id
== wire.destination.allowable_field_type.sample_type_id
)
assert (
wire.source.allowable_field_type.object_type_id
== wire.destination.allowable_field_type.object_type_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_raise_exception_if_wiring_two_outputs(session):
canvas = Planner(session)
assert len(canvas.plan.wires) == 0
op1 = canvas.create_operation_by_name("Check Plate", category="Cloning")
op2 = canvas.create_operation_by_name("Check Plate", category="Cloning")
with pytest.raises(PlannerException):
canvas.add_wire(op1.outputs[0], op2.outputs[0])
def test_quick_wire_to_input_array_and_then_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")
assemble = canvas.create_operation_by_name("Assemble Plasmid", category="Cloning")
canvas.quick_wire(purify1, assemble)
canvas.quick_wire(purify2, assemble)
canvas.set_field_value_and_propogate(purify1.inputs[0], sample=frags[0])
input_array = assemble.input_array("Fragment")
print("purify1: " + str(purify1.rid))
print("purify2: " + str(purify2.rid))
for i in input_array:
print(
i.operation.operation_type.name
+ " "
+ i.name
+ " "
+ str(i.sample)
+ " "
+ str(canvas.get_incoming_wires(i)[0].source.operation.rid)
)
print("ljljklj")
print(purify2.outputs[0].sample)
assert (
assemble.input_array("Fragment")[0].sample == frags[0]
), "Setting a wire should propogate to a field value"
assert assemble.input_array("Fragment")[1].sample is None, (
"Setting a wire should not propogate sample to other field"
"values in the input array."
)
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_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_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_add_successive_operations_with_browser_session(session):
with session.with_cache() as sess:
p = Planner(sess)
p.create_operation_by_name("Make PCR Fragment")
p.create_operation_by_name("Run Gel")
assert len(p.plan.operations) == 2
def test_add_successive_operations(session):
p = Planner(session)
p.create_operation_by_name("Make PCR Fragment")
p.create_operation_by_name("Run Gel")
assert len(p.plan.operations) == 2
def test_quick_chain_to_existing_operation(session):
canvas = Planner(session)
op = canvas.create_operation_by_name("Yeast Transformation")
canvas.chain(op, "Check Yeast Plate")
assert len(canvas.plan.wires) == 1
def test_add_operation_by_name(session):
plan = session.Plan.one()
canvas = Planner(plan)
canvas.create_operation_by_name("Yeast Transformation")