minor fixes and wip user exposures, sources & treatments

Author: adaurat

qmra/risk_assessment/forms.py

@@ -7,6 +7,7 @@
 
 from qmra.risk_assessment.models import Inflow, DefaultTreatments, Treatment, \
     RiskAssessment
+from qmra.user.models import User
 
 
 def _zero_if_none(x): return x if x is not None else 0
@@ -27,7 +28,7 @@ class Meta:
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.fields["source_name"].label = "Select a source water type to add pathogen concentrations"
-        self.fields['exposure_name'].widget.attrs['min'] = 0
+        self.fields['events_per_year'].widget.attrs['min'] = 0
         self.fields['volume_per_event'].widget.attrs['min'] = 0
         self.fields['volume_per_event'].label = "Volume per event in liters"
         self.helper = FormHelper(self)
@@ -39,6 +40,17 @@ def __init__(self, *args, **kwargs):
             # Row("source_name", css_id="source-form")
         )
 
+    def set_user(self, user: User):
+        self.fields["exposure_name"].widget.choices = [
+            ["Your Exposures", [(e.name, e.name) for e in user.exposures.all()]],
+            *self.fields["exposure_name"].widget.choices
+        ]
+        self.fields["source_name"].widget.choices = [
+            ["Your Sources", [(s.name, s.name) for s in user.sources.all()]],
+            *self.fields["source_name"].widget.choices
+        ]
+        return self
+
     def clean(self):
         cleaned_data = super().clean()
         if cleaned_data["events_per_year"] <= 0:
@@ -139,7 +151,7 @@ def __init__(self, *args, **kwargs):
         self.helper.form_tag = False
         self.helper.disable_csrf = True
         self.helper.label_class = "text-muted small"
-        self.fields['name'].choices = DefaultTreatments.choices()
+        # self.fields['name'].choices = DefaultTreatments.choices()
         self.fields['name'].label = ""
         self.fields['bacteria_min'].label = ""
         self.fields['bacteria_max'].label = ""
@@ -201,6 +213,13 @@ def __init__(self, *args, **kwargs):
             "select_treatment",
         )
 
+    def set_user(self, user: User):
+        self.fields["select_treatment"].choices = [
+            *self.fields["select_treatment"].choices,
+            *[(t.name, t.name) for t in user.treatments.all()]
+        ]
+        return self
+
 
 class TreatmentFormSet(TreatmentFormSetBase):
 
@@ -210,3 +229,10 @@ def __init__(self, *args, **kwargs):
         self.helper.form_tag = False
         if not kwargs.get("queryset", False):
             self.queryset = Treatment.objects.none()
+
+    def set_user(self, user: User):
+        self.form.base_fields["name"].choices = [
+            *self.form.base_fields['name'].choices,
+            *[(t.name, t.name) for t in user.treatments.all()]
+        ]
+        return self

qmra/risk_assessment/migrations/0003_userexposure_usersource_usertreatment.py

@@ -0,0 +1,56 @@
+# Generated by Django 5.0.6 on 2025-02-05 06:54
+
+import django.db.models.deletion
+import uuid
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('risk_assessment', '0002_alter_inflow_pathogen_and_more'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='UserExposure',
+            fields=[
+                ('id', models.UUIDField(default=uuid.uuid4, editable=False, primary_key=True, serialize=False)),
+                ('name', models.TextField()),
+                ('description', models.TextField()),
+                ('events_per_year', models.IntegerField()),
+                ('volume_per_event', models.FloatField()),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='exposures', to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='UserSource',
+            fields=[
+                ('id', models.UUIDField(default=uuid.uuid4, editable=False, primary_key=True, serialize=False)),
+                ('name', models.TextField(max_length=64)),
+                ('rotavirus_min', models.FloatField(blank=True, null=True)),
+                ('rotavirus_max', models.FloatField(blank=True, null=True)),
+                ('campylobacter_min', models.FloatField(blank=True, null=True)),
+                ('campylobacter_max', models.FloatField(blank=True, null=True)),
+                ('cryptosporidium_min', models.FloatField(blank=True, null=True)),
+                ('cryptosporidium_max', models.FloatField(blank=True, null=True)),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='sources', to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='UserTreatment',
+            fields=[
+                ('id', models.UUIDField(default=uuid.uuid4, editable=False, primary_key=True, serialize=False)),
+                ('name', models.TextField(max_length=64)),
+                ('bacteria_min', models.FloatField(blank=True, null=True)),
+                ('bacteria_max', models.FloatField(blank=True, null=True)),
+                ('viruses_min', models.FloatField(blank=True, null=True)),
+                ('viruses_max', models.FloatField(blank=True, null=True)),
+                ('protozoa_min', models.FloatField(blank=True, null=True)),
+                ('protozoa_max', models.FloatField(blank=True, null=True)),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='treatments', to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+    ]

qmra/risk_assessment/plots.py

@@ -6,21 +6,22 @@
 RISK_CATEGORY_BG_COLORS = dict(
     none='#E2FBAC', min='#FFDDB5', max='#FFECF4'
 )
-MAX_COLOR_SEQ = ["#FF0532",
-                 "#FF506F",
-                 "#FF8DA2"
-                 ]
+MAX_COLOR_SEQ = [
+    "hsl(359, 100%, 40%)",
+    "hsl(359, 100%, 60%)",
+    "hsl(359, 100%, 80%)",
+]
 
 MIN_COLOR_SEQ = [
-    "#FF873F",
-    "#FFA570",
-    "#ED5500"
+    "hsl(23, 100%, 50%)",
+    "hsl(23, 100%, 70%)",
+    "hsl(23, 100%, 90%)",
 ]
 
 NONE_COLOR_SEQ = [
-    "#1B6638",
-    "#46A16A",
-    "#88D0A5"
+    "hsl(144, 100%, 40%)",
+    "hsl(144, 100%, 60%)",
+    "hsl(144, 100%, 80%)",
 ]
 
 COLOR_SEQS = dict(min=MIN_COLOR_SEQ, max=MAX_COLOR_SEQ, none=NONE_COLOR_SEQ)
@@ -40,6 +41,7 @@ def risk_plots(risk_assessment_results, output_type="div"):
             name=r.pathogen,
             marker=dict(color=COLOR_SEQS[r.infection_risk][i % 3])
         ))
+        # infection_prob_fig.add_annotation(text=r.pathogen, showarrow=False, xref="paper", yref="paper", x=(i+1)/7, y=0)
         dalys_fig.add_trace(go.Box(
             x=["Minimum LRV", "Maximum LRV"],
             lowerfence=[r.dalys_minimum_lrv_min, r.dalys_maximum_lrv_min],
@@ -50,6 +52,7 @@ def risk_plots(risk_assessment_results, output_type="div"):
             name=r.pathogen,
             marker=dict(color=COLOR_SEQS[r.dalys_risk][i % 3])
         ))
+        # dalys_fig.add_annotation(text=r.pathogen, showarrow=False, xref="paper", yref="paper", x=(i+1)/7, y=0)
 
     infection_prob_fig.update_layout(
         boxmode='group',
@@ -60,15 +63,18 @@ def risk_plots(risk_assessment_results, output_type="div"):
         xaxis=dict(title="", showgrid=False),
         yaxis=dict(title="Probability of infection per year",
                    showgrid=False),
-        margin=dict(l=0, r=0, t=30, b=30),
+        margin=dict(l=(int(output_type == "png") * 30), r=(int(output_type == "png") * 30), t=30, b=30),
         legend=dict(
             orientation="h",
             yanchor="top",
             xanchor="center",
             x=0.5,
         )
     )
-    infection_prob_fig.update_yaxes(type="log")
+    infection_prob_fig.update_yaxes(type="log",
+                                    showexponent='all',
+                                    exponentformat='power'
+                                    )
     infection_prob_fig.add_hline(y=0.0001, line_dash="dashdot",
                                  label=dict(
                                      text="tolerable level",
@@ -90,15 +96,18 @@ def risk_plots(risk_assessment_results, output_type="div"):
         plot_bgcolor="#F6F6FF",
         xaxis=dict(title="", showgrid=False),
         yaxis=dict(title="DALYs pppy", showgrid=False),
-        margin=dict(l=0, r=0, t=30, b=30),
+        margin=dict(l=(int(output_type == "png") * 30), r=(int(output_type == "png") * 30), t=30, b=30),
         legend=dict(
             orientation="h",
             yanchor="top",
             xanchor="center",
             x=0.5,
         )
     )
-    dalys_fig.update_yaxes(type="log")
+    dalys_fig.update_yaxes(type="log",
+                           showexponent='all',
+                           exponentformat='power'
+                           )
     dalys_fig.add_hline(y=0.000001, line_dash="dashdot",
                         label=dict(
                             text="tolerable level",