def test_topo_sort_with_independent_subgraphs(self, session):
canvas = Planner(session)
ops1 = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
category="Cloning",
)
ops2 = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
category="Cloning",
)
ops3 = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
category="Cloning",
)
canvas.layout.topo_sort()
print([op.x for op in ops1])
print([op.x for op in ops2])
print([op.x for op in ops3])
assert ops3[0].x + canvas.layout.BOX_DELTA_X == ops2[0].x
assert ops2[0].x + canvas.layout.BOX_DELTA_X == ops1[0].x
def test_align_x_with_predecessors(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
new_ops = canvas.get_op_by_name("E Coli Lysate")
print(len(new_ops))
for _ in range(3):
print("created")
canvas.chain(ops[-1], "E Coli Lysate", category="Cloning")
new_ops = canvas.get_op_by_name("E Coli Lysate")
print(len(new_ops))
new_ops[0].x = 0
new_ops[1].x = 100
new_ops[2].x = 150
ops_layout = canvas.layout.ops_to_subgraph(ops)
new_op_layout = canvas.layout.ops_to_subgraph(new_ops)
midpoint = new_op_layout.midpoint()
assert midpoint[0] == 75, "should be midpoint between 0 and 150"
assert midpoint[0] != ops_layout.midpoint()[0]
new_op_layout.align_x_midpoints_to(ops_layout)
for op in new_op_layout.operations:
print(op.rid)
print(op.x)
print()
assert new_op_layout.midpoint()[0] == ops_layout.midpoint()[0]
def test_quick_wire_to_input_array(session):
canvas = Planner(session)
ops = canvas.chain("Purify Gel Slice", "Assemble Plasmid", category="Cloning")
canvas.chain("Purify Gel Slice", ops[-1], category="Cloning")
assert len(canvas.plan.operations) == 3
assert len(canvas.plan.wires) == 2
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_topo_sort(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
ops[-1].x = 500
for _ in range(3):
canvas.chain(ops[-1], ("E Coli Lysate", "Cloning"), "E Coli Colony PCR")
lysate = canvas.get_op_by_name("E Coli Lysate")
pcr = canvas.get_op_by_name("E Coli Colony PCR")
canvas.layout.ops_to_subgraph(pcr).translate(100, 100)
assert not canvas.layout.ops_to_subgraph(lysate).midpoint()[0] == ops[-1].x
assert (
not canvas.layout.ops_to_subgraph(lysate).midpoint()[0]
== canvas.layout.ops_to_subgraph(pcr).midpoint()[0]
)
canvas.layout.topo_sort()
assert canvas.layout.ops_to_subgraph(lysate).midpoint()[0] == ops[-1].x
assert (
canvas.layout.ops_to_subgraph(lysate).midpoint()[0]
== canvas.layout.ops_to_subgraph(pcr).midpoint()[0]
)
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_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_canvas_quick_create_chain(session):
canvas = Planner(session)
canvas.chain(
"Yeast Transformation", "Check Yeast Plate", "Yeast Overnight Suspension"
)
assert len(canvas.plan.operations) == 3
assert len(canvas.plan.wires) == 2, "There should be two operations"
def planner_example(session):
num_chains = 4
with session.with_cache() as sess:
p = Planner(sess)
for _ in range(num_chains):
p.chain("Make PCR Fragment", "Run Gel", "Extract Gel Slice",
"Purify Gel Slice")
p.plan.id = 1234
return p
def test_layout(self, session):
canvas = Planner(session)
canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
assert canvas.layout is not None
def test_layout_edges_and_nodes(session):
canvas = Planner(session)
canvas.chain(
"Yeast Transformation", "Check Yeast Plate", "Yeast Overnight Suspension"
)
G = canvas.layout.nxgraph
edges = list(G.edges)
assert len(edges) == 2, "There should only be 2 edges/wires in the graph/plan"
assert (
len(G.nodes) == 3
), "There should only be 3 nodes/Operations in the graph/plan"
assert edges[0][1] == edges[1][0], "Check Yeast Plate should be in both wires"
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_roots(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
canvas.chain(
ops[0],
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
assert len(canvas.layout.roots()) == 1
def test_canvas_chaining(session):
canvas = Planner(session)
canvas.browser.log.set_verbose(True)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
assert len(canvas.plan.wires) == 3
new_ops = []
for i in range(3):
new_ops += canvas.chain(
ops[-1], ("E Coli Lysate", "Cloning"), "E Coli Colony PCR"
)[1:]
assert len(canvas.plan.wires) == 2 * 3 + 3
def test_predecessor_layout(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
new_ops = []
for _ in range(3):
new_ops += canvas.chain(
ops[-1], ("E Coli Lysate", "Cloning"), "E Coli Colony PCR"
)[1:]
assert len(new_ops) == 6
predecessor_layout = canvas.layout.predecessor_subgraph(
canvas.layout.ops_to_subgraph(new_ops)
)
assert len(predecessor_layout) == 1
def test_collect_predecessors(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
s = canvas.layout.collect_predecessors(["r{}".format(ops[1].rid)])
assert s == ["r{}".format(ops[0].rid)]
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
def test_align_midpoints(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
new_ops = []
for _ in range(3):
new_ops += canvas.chain(
ops[-1], ("E Coli Lysate", "Cloning"), "E Coli Colony PCR"
)[1:]
layout = canvas.layout.ops_to_subgraph(ops)
successors = canvas.layout.successor_subgraph(layout)
ops[-1].x = 400
successors.align_x_midpoints_to(layout)
assert successors.midpoint()[0] == layout.midpoint()[0]
def test_subgraph(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
graph = canvas.layout.ops_to_subgraph(ops[-2:])
assert len(graph) == 2
canvas.layout.topo_sort()
def test_optimization_case4(self, session):
"""This tests that, even if an operation has the same field_value
settings, if one of its input wires is wired from a different
operation_type, it will not be merged."""
with session.with_cache() as sess:
canvas = Planner(sess)
q = self.sql({
"object_type_id":
sess.ObjectType.find_by_name("Plasmid Glycerol Stock").id,
"location":
self.Not("deleted"),
})
item = sess.Item.one(query=q)
chain1 = [
"Check Plate",
"Make Overnight Suspension",
"Make Miniprep",
"Plasmid Digest",
]
chain2 = [
"Make Overnight Suspension", "Make Miniprep", "Plasmid Digest"
]
ops = canvas.chain(*chain1)
canvas.set_field_value_and_propogate(ops[-1].outputs[0],
sample=item.sample)
ops = canvas.chain(*chain2)
canvas.set_field_value_and_propogate(ops[0].inputs[0], item=item)
assert len(canvas.operations) == 7
canvas.optimize()
assert len(canvas.operations) == 7
def test_routing_graph(session):
canvas = Planner(session)
ops = canvas.chain(
"Rehydrate Primer",
"Make PCR Fragment",
"Run Gel",
"Extract Gel Slice",
"Purify Gel Slice",
"Assemble Plasmid",
category="Cloning",
)
routing_graph = canvas._routing_graph()
print(get_subgraphs(routing_graph))
def test_topo_sort_chain(self, session):
canvas = Planner(session)
ops = canvas.chain(
"Assemble Plasmid",
"Transform Cells",
"Plate Transformed Cells",
"Check Plate",
category="Cloning",
)
ops[-1].x = 300
ops[-2].x = 200
ops[-3].x = 100
assert not len({op.x for op in ops}) == 1
canvas.layout.topo_sort()
assert len({op.x for op in ops}) == 1
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_annotate_layout(session):
canvas = Planner(session)
ops = canvas.chain("Make PCR Fragment", "Run Gel", category="Cloning")
canvas.layout.topo_sort()
canvas.layout.move(100, 200)
a = canvas.annotate_above_layout("This is an annotation", 100, 50)
anchor = a["anchor"]
xmidpoint = a["x"] + anchor["x"] / 2
ybottom = a["y"] + anchor["y"]
assert xmidpoint == 100 + canvas.layout.BOX_WIDTH / 2
assert ybottom == 200 - canvas.layout.BOX_DELTA_Y / 2
canvas.plan.name = "annotation test"
canvas.create()
print(canvas.url)
def test_set_output_and_propogate(session):
session.set_verbose(True)
canvas = Planner(session)
ops = canvas.chain(
"Rehydrate Primer",
"Make PCR Fragment",
"Run Gel",
"Extract Gel Slice",
"Purify Gel Slice",
"Assemble Plasmid",
category="Cloning",
)
example_fragment = session.Sample.find_by_name("SV40-dCas9-split")
canvas.set_output_sample(
ops[1].outputs[0],
sample=example_fragment,
setter=canvas.set_field_value_and_propogate,
)
canvas.validate()
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]
def test_chain_run_gel(session):
canvas = Planner(session)
canvas.chain("Make PCR Fragment", "Run Gel", category="Cloning")
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
