debug manual experiment creation

escalate/core/templates/core/create_experiment.html

@@ -139,11 +139,7 @@ <h6 class="pt-3 pl-3">Reaction Parameters for {{ selected_exp_template.descripti
                     </div>
                       <br>             
                     {% endfor %}
-
-                {{ robot_file_upload_form|crispy }}
-                <button class="btn btn-outline-primary" type="submit" name="robot_upload" value="create_exp">Create Experiment</button> 
 
-
                 <div class="treeview-animated border mx-3 my-4">
                   <h6 class="pt-3 pl-3">Vessel Selection for {{ selected_exp_template.description }}</h6>
                   <hr>
@@ -192,17 +188,13 @@ <h6 class="pt-3 pl-3">Reaction Parameters for {{ selected_exp_template.descripti
                       {% endfor %}
                 </ul>
             </div>
-              <input type="hidden" id="automated" name="automated" value="{{ automated }}">
-              <div class="text-right">
-                <button class="btn btn-outline-primary" type="submit" name="create_exp" value="create_exp">Create Experiment</button>
-              {% endif %}
-
-                </div>
+                {{ robot_file_upload_form|crispy }}
+                <button class="btn btn-outline-primary" type="submit" name="robot_upload" value="create_exp">Create Experiment</button> 
 
         </div>
 
     </div>
-
+        {% endif %}
       {% endif %}
     {% endif %}
 

escalate/core/utilities/calculations.py

@@ -2,7 +2,7 @@
 import requests
 from pint import UnitRegistry
 
-from core.models.view_tables.chemistry_data import ReagentMaterial
+from core.models.view_tables.chemistry_data import ReagentMaterial, Reagent
 from core.models.view_tables import ExperimentInstance
 
 # from core.utilities.experiment_utils import get_action_parameter_querysets

escalate/core/utilities/experiment_utils.py

@@ -456,26 +456,56 @@ def generate_experiments_and_save(
     return q1
 
 
-def save_manual_volumes(df, experiment_copy_uuid):
+def save_manual_volumes(df, experiment_copy_uuid, dead_volume):
     q1 = get_action_parameter_querysets(experiment_copy_uuid, template=False)
     experiment = ExperimentInstance.objects.get(uuid=experiment_copy_uuid)
+    reagents = Reagent.objects.filter(experiment=experiment_copy_uuid)
+
+    if "workflow 1" in experiment.parent.description.lower():
+
+        reagent_action_map = {
+            "Reagent1 (ul)": "dispense solvent",
+            "Reagent7 (ul)": "dispense acid volume 1",
+            "Reagent8 (ul)": "dispense acid volume 2",
+            "Reagent2 (ul)": "dispense stock a",
+            "Reagent3 (ul)": "dispense stock b",
+        }
 
-    reagent_action_map = {
-        "Reagent1 (ul)": "dispense solvent",
-        "Reagent7 (ul)": "dispense acid volume 1",
-        "Reagent8 (ul)": "dispense acid volume 2",
-        "Reagent2 (ul)": "dispense stock a",
-        "Reagent3 (ul)": "dispense stock b",
-    }
+        reagent_template_robot_map = {
+                "Reagent 1 - Solvent": "Reagent1 (ul)",
+                "Reagent 7 - Acid": "Reagent7 (ul)",
+                "Reagent 2 - Stock A": "Reagent2 (ul)",
+                "Reagent 3 - Stock B": "Reagent3 (ul)",
+            }
+
+    elif "workflow 3" in experiment.parent.description.lower():
+        reagent_action_map = {
+            "Reagent1 (ul)": "dispense solvent",
+            "Reagent7 (ul)": "dispense acid volume 1",
+            "Reagent8 (ul)": "dispense acid volume 2",
+            "Reagent2 (ul)": "dispense stock a",
+            "Reagent3 (ul)": "dispense stock b",
+            "Reagent9 (ul)": "dispense antisolvent",
+        }
+
+        reagent_template_robot_map = {
+                "Reagent 1 - Solvent": "Reagent1 (ul)",
+                "Reagent 7 - Acid": "Reagent7 (ul)",
+                "Reagent 2 - Stock A": "Reagent2 (ul)",
+                "Reagent 3 - Stock B": "Reagent3 (ul)",
+                "Reagent 9 - Antisolvent": "Reagent9 (ul)",
+            }
 
     for reagent_name, action_description in reagent_action_map.items():
         well_list = []
         for well in df["Vial Site"]:
             well_list.append(well)
+
+        total_volume=0
 
         for i, vial in enumerate(well_list):
             # get actions from q1 based on keys in action_reagent_map
-            if experiment.parent.ref_uid == "workflow_1":
+            if experiment.parent.ref_uid == "workflow_1" or experiment.parent.ref_uid == "workflow_3":
                 action = q1.get(
                     action_unit_description__icontains=action_description,
                     action_unit_description__endswith=vial,
@@ -495,3 +525,21 @@ def save_manual_volumes(df, experiment_copy_uuid):
             parameter.parameter_val_nominal.value = df[reagent_name][i]
             # parameter.parameter_val_nominal.value = desired_volume[reagent_name][i]
             parameter.save()
+            total_volume+=df[reagent_name][i]
+
+        for reagent in reagents:
+            if reagent_name == reagent_template_robot_map[reagent.template.description]:
+            #if robot_api_map[reagent_name]== reagent.description:
+
+                prop = reagent.property_r.get(
+                        property_template__description__icontains="total volume"
+                    )
+                prop.nominal_value.value = total_volume
+                prop.nominal_value.unit = "uL"
+                prop.save()
+                if dead_volume is not None:
+                    dv_prop = reagent.property_r.get(
+                        property_template__description__icontains="dead volume"
+                    )
+                    dv_prop.nominal_value = dead_volume
+                    dv_prop.save()

escalate/core/views/experiment/create.py

@@ -50,6 +50,7 @@
     save_manual_volumes,
     save_parameter,
 )
+from core.utilities.calculations import conc_to_amount
 from core.utilities.wf1_utils import generate_robot_file_wf1
 from core.models.view_tables.generic_data import Parameter
 
@@ -391,17 +392,58 @@ def process_robot_formsets(self, exp_uuid, request, context):
             exp_concentrations = {}
             for reagent_formset in formsets:
                 if reagent_formset.is_valid():
-                    # vector = self.save_forms_reagent(reagent_formset, experiment_copy_uuid, exp_concentrations)
+                    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.value
+            else:
+                dead_volume = None
 
+            # post reaction parameter form
+            # get label here and get form out of label, use label for description
+            rp_wfs = get_action_parameter_querysets(exp_template.uuid)
+            index = 0
+            for rp in rp_wfs:
+                rp_label = str(rp.object_description)
+                if "Dispense" in rp_label:
+                    continue
+                else:
+                    rp_form = ReactionParameterForm(
+                        request.POST, prefix=f"reaction_parameter_{index}"
+                    )
+                    if rp_form.is_valid:
+                        rp_value = rp_form.data[f"reaction_parameter_{index}-value_0"]
+                        rp_unit = rp_form.data[f"reaction_parameter_{index}-value_1"]
+                        rp_type = rp_form.data[f"reaction_parameter_{index}-value_2"]
+                        rp_uuid = rp_form.data[f"reaction_parameter_{index}-uuid"]
+                        save_reaction_parameters(
+                            exp_template,
+                            rp_value,
+                            rp_unit,
+                            rp_type,
+                            rp_label,
+                            experiment_copy_uuid,
+                        )
+                        # The rp_uuid is not being generated from the loadscript for some parameters
+                        # This issue stems from the data being loaded in. This function will work once we fix loading issues
+                        if rp_uuid != "":
+                            save_parameter(rp_uuid, rp_value, rp_unit)
+                    index += 1
+
+
+
         df = pd.read_excel(request.FILES["file"])
         # self.process_robot_file(df)
-        save_manual_volumes(df, experiment_copy_uuid)
+        save_manual_volumes(df, experiment_copy_uuid, dead_volume)
+
+        conc_to_amount(experiment_copy_uuid)
 
         context["experiment_link"] = reverse(
             "experiment_instance_view", args=[experiment_copy_uuid]