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Revert "Revert "fixed dead volume form and acid concentration calculations"" #192

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Dec 7, 2021
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Revert "Revert "fixed dead volume form and acid concentration calculations"" #192

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2 changes: 1 addition & 1 deletion escalate/core/forms/custom_types.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ def get_helper():

class SingleValForm(Form):
value = ValFormField(required=False)
uuid = CharField(widget=HiddenInput)
uuid = CharField(widget=HiddenInput, required=False)


class RobotForm(Form):
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59 changes: 33 additions & 26 deletions escalate/core/utilities/calculations.py
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Expand Up @@ -35,6 +35,7 @@ def conc_to_amount(exp_uuid):
conc_val = conc.nominal_value.value
conc_unit = conc.nominal_value.unit
conc = Q_(conc_val, conc_unit)
mat_type=reagent_material.template.material_type.description
phase = reagent_material.material.phase
if not phase:
raise ValueError(
Expand All @@ -53,6 +54,7 @@ def conc_to_amount(exp_uuid):

input_data[reagent_material] = {
"concentration": conc,
"material_type": mat_type,
"phase": phase,
"molecular weight": mw,
"density": d,
Expand Down Expand Up @@ -180,28 +182,20 @@ def generate_input_f(reagent, MW, density):
return input_data


def calculate_amounts(input_data, target_vol, dead_vol="3000 uL"):
def calculate_amounts(input_data, target_vol, dead_vol="4000 uL"):

"""
Given input data from helper function and target/dead volumes (strings with units),
Given input data dictionary for reagents and target/dead volumes,
returns amounts of each reagent component needed to achieve desired concentrations.
For solids/solutes, amounts will be reported in grams.
For liquid/solvent, amount will be reported in mL.
For liquid/solvent/acid, amount will be reported in mL.

"""

# input_data comes from helper function above
# target_vol and dead_vol must be input as strings with units

amounts = {}
amounts = {}
exact_amounts = {} #use this to store exact values for more precise calculations

# convert volumes to mL and store in proper Pint format
# mag_t=float(total_vol.split()[0])
# unit_t= str(total_vol.split()[1])

# mag_d=float(dead_vol.split()[0])
# unit_d=str(dead_vol.split()[1])

vol = Q_(target_vol).to(units.ml)
dead = Q_(dead_vol).to(units.ml)
total_vol = vol + dead
Expand All @@ -214,22 +208,35 @@ def calculate_amounts(input_data, target_vol, dead_vol="3000 uL"):
* val["molecular weight"]
)
# convert concentration to moles to mass
exact_amounts[key] = grams
amounts[key] = round(grams, 2)

for substance, amount in amounts.items(): # for all solids
total_vol -= amount / input_data[substance]["density"] # find the volume
# find the volume. subtract from total volume - this is how much liquid will be needed

for key, val in input_data.items():
if val["phase"] == "liquid":
if val["material_type"]=="acid": # for the acids
neat=((100/val["molecular weight"])/ (100/val['density'])).to(units.mol/units.ml) #concentration of neat (pure) acid
vol= total_vol* val["concentration"].to(units.mol / units.ml)/neat #dilution
exact_amounts[key]=vol
amounts[key]=round(vol, 2)

for substance, amount in exact_amounts.items():
# for solids
if input_data[substance]["phase"]=='solid':
total_vol -= amount / input_data[substance]["density"] # find the volume and subtract from total

#for acids
elif input_data[substance]["phase"]=='liquid':
total_vol -= vol # find the volume and subtract from total

for key, val in input_data.items():
if val["phase"] == "liquid": # for the solvent(s)
if "volume fraction" in val.keys(): # if there is more than one solvent
amounts[key] = round(
total_vol * val["volume fraction"], 2
) # amount is a fraction of the remaining available volume
else: # if there's just one solvent
amounts[key] = round(
total_vol, 2
) # amount is the remaining available volume
if val["phase"] == "liquid":
if val["material_type"]!="acid": #for the solvent(s)
if "volume fraction" in val.keys(): # if there is more than one solvent
amounts[key] = round(
total_vol * val["volume fraction"], 2
) # amount is a fraction of the remaining available volume
else: #if there is just one solvent
amounts[key] = round(total_vol, 2) # amount is the remaining available volume

"""
for key, val in amounts.items(): #convert amounts from Pint format to strings with val and unit
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18 changes: 14 additions & 4 deletions escalate/core/views/experiment/create.py
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Expand Up @@ -621,9 +621,18 @@ def process_robot_formsets(self, exp_uuid, request, context):
for reagent_formset in formsets:
if reagent_formset.is_valid():
vector = self.save_forms_reagent(reagent_formset, experiment_copy_uuid, exp_concentrations)
#exp_concentrations = prepare_reagents(
#reagent_formset, exp_concentrations
#)
#try:
exp_concentrations = prepare_reagents(
reagent_formset, exp_concentrations
)
#except TypeError as te:
# messages.error(request, str(te))

dead_volume_form = SingleValForm(request.POST, prefix="dead_volume")
if dead_volume_form.is_valid():
dead_volume = dead_volume_form.cleaned_data['value']
else:
dead_volume = None

# post reaction parameter form
# get label here and get form out of label, use label for description
Expand Down Expand Up @@ -937,7 +946,8 @@ def process_automated_formsets(self, request: HttpRequest, context: dict[str, An
# Save dead volumes should probably be in a separate function
dead_volume_form = SingleValForm(request.POST, prefix="dead_volume")
if dead_volume_form.is_valid():
dead_volume = dead_volume_form.value
dead_volume=dead_volume_form.cleaned_data['value']
#dead_volume = dead_volume_form.value
else:
dead_volume = None

Expand Down