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_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_optimize_case4_array_inputs(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:])) for ops in [ops1, ops2, ops3, ops4]: pour_gel = canvas.chain("Pour Gel", ops[1])[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]) 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() op_types = sorted( [op.operation_type.name for op in canvas.operations]) print(op_types) assert len(canvas.get_op_by_name("Assemble Plasmid")) == 1 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) == 2 for input_fv in op.inputs: assert len(canvas.get_incoming_wires(input_fv)) == 1 assert len(canvas.get_op_by_name("Pour Gel")) == 2