Experiment Planning

Trident provides a class to help with creating Aquarium plans, called the “planner”

Features: topological sorting, plan optimizer, drawing

You can draw existing plans (colors represent Operation statuses, legend to come…):

%matplotlib inline

from pydent import planner
canvas = planner.Planner(mysession, plan_id=12345)
canvas.layout.draw()

Example of planning a large PCR in a IPython jupyter notebook.

%matplotlib inline
from pydent import planner
from mysession import production

sample_range = list(range(25589, 25604))
canvas = planner.Planner(production)

def set_primer(canvas, field_value, sample):
    canvas.set_field_value(field_value, sample=sample)
    items = [item for item in sample.items if item.location != 'deleted']
    primer_stocks = [item for item in items if item.object_type.name == "Primer Stock"]
    primer_aliquots = [item for item in items if item.object_type.name == "Primer Aliquot"]

    if len(primer_aliquots) > 0:
        # set item
        canvas.set_field_value(field_value, sample=sample, item=primer_aliquots[-1])
        return
    else:
        print("No primer aliquots found for {}".format(sample.name))
        if len(primer_stocks) > 0:
            # create Make Primer Aliquot from Stock
            op = canvas.create_operation_by_name("Make Primer Aliquot from Stock")
            canvas.add_wire(op.outputs[0], field_value)
            canvas.set_field_value(ops[0].inputs[0], sample=sample, item=primer_stocks[-1])
            return
        else:
            print("No primer stocks found for {}".format(sample.name))
            # create Order Primer and Rehydrate Primer
            op = canvas.create_operation_by_name("Order Primer")

            canvas.set_field_value(op.inputs[0], value="yes")
            canvas.set_field_value(op.outputs[0], sample=field_value.sample)
            ops = canvas.quick_create_chain(op, "Rehydrate Primer")
            canvas.add_wire(ops[1].outputs[0], field_value)
            return


def submit_pcr(canvas, sample):
    op = canvas.create_operation_by_name("Make PCR Fragment")
    canvas.set_field_value(op.outputs[0], sample=sample)

    fwd = sample.properties['Forward Primer']
    rev = sample.properties['Reverse Primer']
    template = sample.properties['Template']

    set_primer(canvas, op.input("Forward Primer"), fwd)
    set_primer(canvas, op.input("Reverse Primer"), rev)

    canvas.set_field_value(op.input("Template"), sample=template)

    new_ops = canvas.quick_create_chain(op, "Run Gel", "Extract Gel Slice", "Purify Gel Slice")
    run_gel = new_ops[1]
    canvas.quick_create_chain("Pour Gel", run_gel)


from pydent.utils import make_async

@make_async(chunk_size=1, progress_bar=False)
def submit_pcrs(sample_range):
    for sample_id in sample_range:
        submit_pcr(canvas, production.Sample.find(sample_id))
    return []

# submit PCR asynchrounous to the canvas
submit_pcrs(sample_range)

# optimize the plan
canvas.optimize()

# topologically sort the layout
canvas.layout.topo_sort()

# draw the layout
canvas.layout.draw()

# push the plan to Aquarium
canvas.create()

# display the Aquarium plan url
canvas.url