Merge pull request #156 from ImperialCollegeLondon/chem-calc

Calculation of formula mass

dfndb/forms.py

@@ -25,6 +25,13 @@ class NewCompoundForm(DataCreateForm):
     class Meta:
         model = Compound
         fields = ["name", "formula", "mass"]
+        help_texts = {
+            "formula": "Chemical formula. This will be used to calculate the mass.",
+            "mass": (
+                "Only fill in if the formula should not be used to automatically "
+                " calculate the mass. Otherwise, leave as 0."
+            ),
+        }
 
     def __init__(self, *args, **kwargs):
         super(NewCompoundForm, self).__init__(*args, **kwargs)
@@ -34,8 +41,15 @@ def __init__(self, *args, **kwargs):
                 Div(HTML("<h1> Compound </h1>")),
                 Div(
                     HTML(
-                        """Note: compounds should be specified in their discharged state, 
-                        if relevant, and are always public (visible to all users)."""
+                        """
+                        Compounds should be specified in their discharged state
+                        (if relevant) and are always public (visible to all users).
+                        The mass is calculated automatically from the formula unless
+                        specified otherwise.
+                        <a href="https://www.sciencegateway.org/tools/fwcal.htm"
+                        target="_blank"> Click here for an external molecular weight
+                        calculator &#10697;</a>.
+                        """
                     ),
                     css_class="container py-2",
                 ),

dfndb/models.py

@@ -4,6 +4,7 @@
 from django.db.models import Sum
 from django.urls import reverse
 from django_better_admin_arrayfield.models.fields import ArrayField
+from molmass import Formula
 
 import common.models as cm
 
@@ -13,7 +14,7 @@ class Compound(models.Model):
 
     name = models.CharField(
         max_length=100,
-        help_text="Full name for the element or compound",
+        help_text="Full name for the element or compound.",
     )
     formula = models.CharField(max_length=20, help_text="Chemical formula")
     mass = models.FloatField(
@@ -25,6 +26,13 @@ class Compound(models.Model):
     def __str__(self):
         return "%s (%s)" % (self.name, self.formula)
 
+    def clean(self):
+        """
+        Use the formula to calculate the mass if not specified.
+        """
+        if self.mass == 0:
+            self.mass = Formula(self.formula).mass
+
     class Meta:
         unique_together = (
             "name",

dfndb/views.py

@@ -1,9 +1,12 @@
+from django.contrib import messages
+from django.shortcuts import redirect, render
 from django.urls import reverse_lazy
 from django.views.generic import DetailView, ListView
 from django_filters.views import FilterView
 from django_tables2 import SingleTableMixin
 from django_tables2.export.views import ExportMixin
 from guardian.mixins import PermissionListMixin, PermissionRequiredMixin
+from molmass import FormulaError
 from rest_framework.generics import ListCreateAPIView
 
 from common.views import (
@@ -31,6 +34,36 @@ class NewCompoundView(PermissionRequiredMixin, NewDataView):
     success_message = "New compound created successfully."
     failure_message = "Could not save new compound. Invalid information."
 
+    def post(self, request, *args, **kwargs):
+        form = self.form_class(request.POST, request.FILES)
+        try:
+            if form.is_valid():
+                obj = form.save(commit=False)
+                # Do other stuff before saving here
+                obj.user_owner = request.user
+                if form.is_public():
+                    obj.status = "public"
+                else:
+                    obj.status = "private"
+                obj.save()
+                messages.success(request, self.success_message)
+                # Redirect to object detail view or stay on form if "add another"
+                if "another" in request.POST:
+                    return redirect(request.path_info)
+                else:
+                    return (
+                        redirect(self.success_url)
+                        if self.success_url
+                        else redirect(obj)
+                    )
+            messages.error(request, self.failure_message)
+        except FormulaError as e:
+            messages.error(
+                request,
+                f"{e} - Formula is not valid. Please check your formula or enter the mass manually.",
+            )
+        return render(request, self.template_name, {"form": form})
+
 
 class NewComponentView(PermissionRequiredMixin, NewDataViewInline):
     permission_required = "dfndb.add_component"
@@ -98,6 +131,36 @@ class UpdateCompoundView(PermissionRequiredMixin, UpdateDataView):
     inline_key = "composition"
     formset = CompositionPartFormSet
 
+    def post(self, request, *args, **kwargs):
+        self.object = self.get_object()
+        form_class = self.get_form_class()
+        form = self.get_form(form_class)
+        try:
+            if form.is_valid():
+                # Do other stuff before saving here
+                if form.is_public():
+                    self.object.status = "public"
+                else:
+                    self.object.status = "private"
+                self.object.save()
+                messages.success(request, self.success_message)
+                # Redirect to object detail view or stay on form if "add another"
+                if "another" in request.POST:
+                    return redirect(request.path_info)
+                else:
+                    return (
+                        redirect(self.success_url)
+                        if self.success_url
+                        else redirect(self.object)
+                    )
+            messages.error(request, self.failure_message)
+        except FormulaError as e:
+            messages.error(
+                request,
+                f"{e} - Formula is not valid. Please check your formula or enter the mass manually.",
+            )
+        return render(request, self.template_name, {"form": form})
+
 
 class DataListView(ListView):
     """View of available data.

requirements.txt

@@ -25,4 +25,5 @@ django-filter
 tablib
 openpyxl
 django-storages[azure]
-django-override-storage
+django-override-storage
+molmass

tests/dfndb/test_models.py

@@ -5,10 +5,11 @@
 
 class TestCompound(TestCase):
     def setUp(self):
-        self.expected = dict(name="Carbon Dioxide", formula="CO2", mass=44.01)
+        self.expected = dict(name="Carbon Dioxide", formula="CO2", mass=44.00955)
         self.model = baker.make_recipe(
-            "tests.dfndb.compound", name="Carbon Dioxide", formula="CO2", mass=44.01
+            "tests.dfndb.compound", name="Carbon Dioxide", formula="CO2"
         )
+        self.model.clean()  # to calculate the mass from the formula
 
     def test_compound_creation(self):
         for k, v in self.expected.items():
@@ -26,6 +27,13 @@ def test_unique_together(self):
                 "tests.dfndb.compound", name="Carbon Dioxide", formula="CO2", mass=44.01
             )
 
+    def test_invalid_formula(self):
+        from molmass import FormulaError
+
+        with self.assertRaises(FormulaError):
+            invalid_comp = baker.make_recipe("tests.dfndb.compound", formula="H2So4")
+            invalid_comp.clean()
+
 
 class TestComponent(TestCase):
     def setUp(self):