Merge pull request #191 from darkreactions/revert-190-nicole_debug_vo…

…lumes

Revert "fixed dead volume form and acid concentration calculations"

escalate/core/forms/custom_types.py

@@ -41,7 +41,7 @@ def get_helper():
 
 class SingleValForm(Form):
     value = ValFormField(required=False)
-    uuid = CharField(widget=HiddenInput, required=False)
+    uuid = CharField(widget=HiddenInput)
 
 
 class RobotForm(Form):

escalate/core/utilities/calculations.py

@@ -35,7 +35,6 @@ 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(
@@ -54,7 +53,6 @@ def conc_to_amount(exp_uuid):
 
             input_data[reagent_material] = {
                 "concentration": conc,
-                "material_type": mat_type,
                 "phase": phase,
                 "molecular weight": mw,
                 "density": d,
@@ -182,20 +180,28 @@ def generate_input_f(reagent, MW, density):
     return input_data
 
 
-def calculate_amounts(input_data, target_vol, dead_vol="4000 uL"):
+def calculate_amounts(input_data, target_vol, dead_vol="3000 uL"):
 
     """
-    Given input data dictionary for reagents and target/dead volumes,
+    Given input data from helper function and target/dead volumes (strings with units),
     returns amounts of each reagent component needed to achieve desired concentrations.
     For solids/solutes, amounts will be reported in grams.
-    For liquid/solvent/acid, amount will be reported in mL.
+    For liquid/solvent, amount will be reported in mL.
 
     """
 
-    amounts = {} 
-    exact_amounts = {} #use this to store exact values for more precise calculations 
+    # input_data comes from helper function above
+    # target_vol and dead_vol must be input as strings with units
+
+    amounts = {}
 
     # 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
@@ -208,35 +214,22 @@ def calculate_amounts(input_data, target_vol, dead_vol="4000 uL"):
                 * val["molecular weight"]
             )
             # convert concentration to moles to mass
-            exact_amounts[key] = grams
             amounts[key] = round(grams, 2)
-
-    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 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 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
+        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
 
     """
     for key, val in amounts.items(): #convert amounts from Pint format to strings with val and unit

escalate/core/views/experiment/create.py

@@ -621,18 +621,9 @@ 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)
-                    #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
+                    #exp_concentrations = prepare_reagents(
+                        #reagent_formset, exp_concentrations
+                    #)
 
             # post reaction parameter form
             # get label here and get form out of label, use label for description
@@ -946,8 +937,7 @@ 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.cleaned_data['value']
-                #dead_volume = dead_volume_form.value
+                dead_volume = dead_volume_form.value
             else:
                 dead_volume = None