def test_optimize(self, session):
with session.with_cache() as sess:
canvas = Planner(sess)
q = self.sql({
"object_type_id":
sess.ObjectType.find_by_name("Plasmid Stock").id,
"location":
self.Not("deleted"),
})
item = sess.Item.one(query=q)
assert item
ops = canvas.chain("Make Miniprep", "Yeast Transformation",
"Yeast Overnight Suspension")
canvas.set_field_value_and_propogate(ops[0].inputs[0],
sample=item.sample)
canvas.set_to_available_item(ops[0].inputs[0])
ops = canvas.chain("Make Miniprep", "Yeast Transformation",
"Yeast Overnight Suspension")
canvas.set_field_value_and_propogate(ops[0].inputs[0],
sample=item.sample)
canvas.set_to_available_item(ops[0].inputs[0])
assert len(canvas.plan.operations) == 6
canvas.optimize()
assert len(canvas.plan.operations) == 5
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_optimize3(self, session):
"""Here we setup two operations chains of 5.
6 of these operations will be mergable (10 to 7). We also add
additional operations to one of the Miniprep operations. We
should end up with 9 operations after the optimization.
Additionally, the merged Miniprep should have a single output
with 3 wires.
"""
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",
]
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])
ops[-1].tagged = "YES"
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.chain(ops[2], "Yeast Transformation")
canvas.chain(ops[2], "Make PCR Fragment")
assert len(canvas.plan.operations) == 12
assert len(canvas.get_outgoing_wires(ops[2].outputs[0])) == 3
canvas.optimize()
assert len(canvas.plan.operations) == 9
assert len(canvas.get_outgoing_wires(ops[2].outputs[0])) == 4
for yt in canvas.get_op_by_name("Yeast Transformation"):
print(yt.inputs[0].name)
assert len(canvas.get_incoming_wires(yt.inputs[0]))
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_prettify(session):
with session.with_cache() as sess:
canvas = Planner(sess)
chain = [
"Check Plate",
"Make Overnight Suspension",
"Make Miniprep",
"Yeast Transformation",
"Yeast Overnight Suspension",
]
ops = canvas.chain(*chain)
canvas.set_field_value_and_propogate(ops[0].inputs[0])
canvas.set_to_available_item(ops[0].inputs[0])
ops = canvas.chain(*chain)
canvas.set_field_value_and_propogate(ops[0].inputs[0])
canvas.set_to_available_item(ops[0].inputs[0])
canvas.prettify()
def test_optimize_with_existing_plan(self, session):
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",
]
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])
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])
assert len(canvas.plan.operations) == 10
canvas.save()
plan_id = canvas.plan.id
with session.with_cache(timeout=60) as sess:
canvas = Planner(sess.Plan.find(plan_id))
canvas.optimize()
assert len(canvas.plan.operations) == 7
