Merge pull request #4 from KWB-R/experimental/plotly-js

presentation version

.dockerignore

@@ -0,0 +1 @@
+**/static

Dockerfile

@@ -8,12 +8,12 @@ WORKDIR qmra
 ENV PYTHONDONTWRITEBYTECODE=1
 ENV PYTHONUNBUFFERED=1
 
-RUN apt update && apt upgrade -y
+RUN apt-get update -y && apt upgrade -y && apt-get clean && rm -rf /var/lib/apt/lists/*
 # install dependencies
-RUN pip install --upgrade pip
 COPY ./requirements.txt .
-RUN pip install -r requirements.txt
-RUN pip install gunicorn
+RUN pip install --upgrade pip &&\
+    pip install --no-cache-dir -r requirements.txt &&\
+    pip install --no-cache-dir gunicorn
 
 # copy project
 COPY ./qmra ./qmra

qmra/management/commands/collect_static_default_entities.py

@@ -6,6 +6,7 @@
 
 def get_default_pathogens():
     pathogen = pd.read_csv("raw_public_data/tbl_pathogen.csv", encoding="windows-1251")
+    pathogen = pathogen[pathogen.id.isin((3, 32, 34))]
     health = pd.read_csv("raw_public_data/tbl_health.csv", encoding="windows-1251")
     # NOTE: HEALTH has been modified 'pathogen_id' is now 'pathogen_group'!!
     #       i.e. Rotavirus -> Viruses, jejuni -> Bacteria, parvum -> Protozoa
@@ -27,6 +28,7 @@ def get_default_inflows():
     sources = pd.read_csv("raw_public_data/tbl_waterSource.csv", encoding="windows-1251")
     inflows = pd.merge(inflows, sources, left_on="source_id", right_on="id", how="left").rename(columns={"name": "source_name"})
     inflows = pd.merge(inflows, pathogens, left_on="pathogen_id", right_on="id", how="left").rename(columns={"name": "pathogen_name"})
+    inflows = inflows[inflows.pathogen_id.isin((3, 32, 34))]
     return inflows.loc[:, ["source_name", "pathogen_name", "min", "max"]]
 
 

qmra/risk_assessment/forms.py

@@ -1,14 +1,17 @@
 from django import forms
 from django.core.exceptions import ValidationError
-from django.forms import modelformset_factory, HiddenInput
-from crispy_forms.bootstrap import AppendedText, Modal
+from django.forms import modelformset_factory
+from crispy_forms.bootstrap import AppendedText
 from crispy_forms.helper import FormHelper
-from crispy_forms.layout import Layout, Field, Row, Column, Div, HTML, Button
+from crispy_forms.layout import Layout, Field, Row, Column, HTML
 
-from qmra.risk_assessment.models import Inflow, DefaultPathogens, DefaultTreatments, Treatment, \
+from qmra.risk_assessment.models import Inflow, DefaultTreatments, Treatment, \
     RiskAssessment
 
 
+def _zero_if_none(x): return x if x is not None else 0
+
+
 class RiskAssessmentForm(forms.ModelForm):
     class Meta:
         model = RiskAssessment
@@ -23,7 +26,7 @@ class Meta:
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.fields["source_name"].label = "Select a source type to add inflows"
+        self.fields["source_name"].label = "Select a source water type to add pathogen concentrations"
         self.fields['exposure_name'].widget.attrs['min'] = 0
         self.fields['volume_per_event'].widget.attrs['min'] = 0
         self.helper = FormHelper(self)
@@ -53,14 +56,15 @@ class Meta:
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+        self.initial.update(kwargs.get("initial", {}))
         self.helper = FormHelper(self)
         self.helper.render_hidden_fields = False
         self.helper.render_unmentioned_fields = False
         self.helper.form_tag = False
         self.helper.disable_csrf = True
         self.helper.label_class = "text-muted small"
-        self.fields['pathogen'].choices = DefaultPathogens.choices()
-        self.fields['pathogen'].label = "Pathogen"
+        self.fields['pathogen'].disabled = True
+        self.fields['pathogen'].label = "Reference Pathogen"
         self.fields['min'].widget.attrs['min'] = 0
         self.fields['max'].widget.attrs['min'] = 0
         self.fields['min'].label = "Minimum concentration"
@@ -75,11 +79,12 @@ def __init__(self, *args, **kwargs):
 
     def clean(self):
         cleaned_data = super().clean()
-        if cleaned_data["min"] < 0:
+        mn, mx = cleaned_data.get("min", 0), cleaned_data.get("max", 0)
+        if mn < 0:
             self.add_error("min", "this field must be positive or 0")
-        if cleaned_data["max"] < 0:
+        if mx < 0:
             self.add_error("max", "this field must be positive or 0")
-        if cleaned_data.get("min", 0) > cleaned_data.get("max", 0):
+        if mn > mx:
             msg = "minimum concentration must be less than maximum concentration"
             self.add_error("min", msg)
             self.add_error("max", msg)
@@ -88,16 +93,19 @@ def clean(self):
 
 InflowFormSetBase = modelformset_factory(
     Inflow, form=InflowForm,
-    extra=0, max_num=30, min_num=0,
-    can_delete=True, can_delete_extra=True
+    extra=0, max_num=3, min_num=3,
+    can_delete=False, can_delete_extra=False
 )
 
 
 class InflowFormSet(InflowFormSetBase):
-    def get_deletion_widget(self):
-        return forms.CheckboxInput(attrs=dict(label="remove"))
 
     def __init__(self, *args, **kwargs):
+        kwargs["initial"] = [
+                    {"pathogen": "Rotavirus"},
+                    {"pathogen": 'Campylobacter jejuni'},
+                    {"pathogen": "Cryptosporidium parvum"},
+                ]
         super().__init__(*args, **kwargs)
         self.helper = FormHelper()
         self.helper.form_tag = False
@@ -146,7 +154,7 @@ def __init__(self, *args, **kwargs):
         self.fields['protozoa_max'].widget.attrs['min'] = 0
         label_style = "class='text-muted text-center w-100' style='margin-top: .4em;'"
         self.helper.layout = Layout(
-            Field("name", css_class="disabled-input text-center"),
+            Field("name", css_class="disabled-input d-none"),
             Row(Column(HTML(f"<div></div>")),
                 Column(HTML(f"<label class='text-muted text-center w-100'>Minimum</label>")),
                 Column(HTML(f"<label class='text-muted text-center w-100'>Maximum</label>"))),
@@ -161,24 +169,30 @@ def __init__(self, *args, **kwargs):
 
     def clean(self):
         cleaned_data = super().clean()
-        if cleaned_data["bacteria_min"] < 0:
+        b_min = _zero_if_none(cleaned_data.get("bacteria_min", 0))
+        b_max = _zero_if_none(cleaned_data.get("bacteria_max", 0))
+        v_min = _zero_if_none(cleaned_data.get("viruses_min", 0))
+        v_max = _zero_if_none(cleaned_data.get("viruses_max", 0))
+        p_min = _zero_if_none(cleaned_data.get("protozoa_min", 0))
+        p_max = _zero_if_none(cleaned_data.get("protozoa_max", 0))
+        if b_min < 0:
             self.add_error("bacteria_min", "this field must be positive or 0")
-        if cleaned_data["bacteria_max"] < 0:
+        if b_max < 0:
             self.add_error("bacteria_max", "this field must be positive or 0")
-        if cleaned_data["viruses_min"] < 0:
+        if v_min < 0:
             self.add_error("viruses_min", "this field must be positive or 0")
-        if cleaned_data["viruses_max"] < 0:
+        if v_max < 0:
             self.add_error("viruses_max", "this field must be positive or 0")
-        if cleaned_data["protozoa_min"] < 0:
+        if p_min < 0:
             self.add_error("protozoa_min", "this field must be positive or 0")
-        if cleaned_data["protozoa_max"] < 0:
+        if p_max < 0:
             self.add_error("protozoa_max", "this field must be positive or 0")
         msg = "min. must be less than max"
-        if cleaned_data.get("bacteria_min", 0) > cleaned_data.get("bacteria_max", 0):
+        if b_min > b_max:
             self.add_error("bacteria_min", msg)
-        if cleaned_data.get("viruses_min", 0) > cleaned_data.get("viruses_max", 0):
+        if v_min > v_max:
             self.add_error("viruses_min", msg)
-        if cleaned_data.get("protozoa_min", 0) > cleaned_data.get("protozoa_max", 0):
+        if p_min > p_max:
             self.add_error("protozoa_min", msg)
         return cleaned_data
 

qmra/risk_assessment/migrations/0002_alter_inflow_pathogen_and_more.py

@@ -0,0 +1,33 @@
+# Generated by Django 5.0.6 on 2024-10-18 14:52
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('risk_assessment', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='inflow',
+            name='pathogen',
+            field=models.CharField(choices=[('', '---------'), ('Bacteria', [('Campylobacter jejuni', 'Campylobacter jejuni')]), ('Viruses', [('Rotavirus', 'Rotavirus')]), ('Protozoa', [('Cryptosporidium parvum', 'Cryptosporidium parvum')])], max_length=256),
+        ),
+        migrations.AlterField(
+            model_name='riskassessmentresult',
+            name='dalys_risk',
+            field=models.CharField(choices=[('min', 'min'), ('max', 'max'), ('none', 'none')], max_length=4),
+        ),
+        migrations.AlterField(
+            model_name='riskassessmentresult',
+            name='infection_risk',
+            field=models.CharField(choices=[('min', 'min'), ('max', 'max'), ('none', 'none')], max_length=4),
+        ),
+        migrations.AlterField(
+            model_name='riskassessmentresult',
+            name='pathogen',
+            field=models.CharField(choices=[('', '---------'), ('Bacteria', [('Campylobacter jejuni', 'Campylobacter jejuni')]), ('Viruses', [('Rotavirus', 'Rotavirus')]), ('Protozoa', [('Cryptosporidium parvum', 'Cryptosporidium parvum')])], max_length=256),
+        ),
+    ]

qmra/risk_assessment/models.py

@@ -198,7 +198,8 @@ class DefaultSources(StaticEntity):
 
     @classmethod
     def choices(cls):
-        grouped = {grp: list(v) for grp, v in groupby(sorted(cls.data.values(), key=lambda x: x.name), key=lambda x: x.name.split(",")[0])}
+        grouped = {grp: list(v) for grp, v in
+                   groupby(sorted(cls.data.values(), key=lambda x: x.name), key=lambda x: x.name.split(",")[0])}
         return [
             ("", "---------"),
             *[(k, [(x.name, x.name) for x in v]) for k, v in grouped.items()],
@@ -294,7 +295,8 @@ class DefaultExposures(StaticEntity):
 
     @classmethod
     def choices(cls):
-        grouped = {grp: list(v) for grp, v in groupby(sorted(cls.data.values(), key=lambda x: x.name), key=lambda x: x.name.split(",")[0])}
+        grouped = {grp: list(v) for grp, v in
+                   groupby(sorted(cls.data.values(), key=lambda x: x.name), key=lambda x: x.name.split(",")[0])}
         return [
             ("", "---------"),
             *[(k, [(x.name, x.name) for x in sorted(v, key=lambda x: x.name)]) for k, v in grouped.items()],
@@ -322,7 +324,8 @@ class RiskAssessment(models.Model):
 
     @property
     def infection_risk(self):
-        return any(r.infection_risk for r in self.results.all())
+        risks = {r.infection_risk for r in self.results.all()}
+        return 'max' if 'max' in risks else ("min" if 'min' in risks else 'none')
 
     @property
     def dalys_risk(self):
@@ -336,6 +339,9 @@ def pathogens_labels(self):
     def treatments_labels(self):
         return ", ".join([treatment.name for treatment in self.treatments.all()])
 
+    def results_list(self):
+        return [r.as_dict() for r in self.results.all()]
+
     def __str__(self):
         return self.name
 
@@ -344,10 +350,8 @@ class RiskAssessmentResult(models.Model):
     risk_assessment = models.ForeignKey(RiskAssessment, on_delete=models.CASCADE, related_name="results")
 
     pathogen = models.CharField(choices=DefaultPathogens.choices(), max_length=256)
-
-    infection_risk = models.BooleanField()
-    dalys_risk = models.BooleanField()
-
+    infection_risk = models.CharField(choices=[("min", "min"), ("max", "max"), ("none", "none")], max_length=4)
+    dalys_risk = models.CharField(choices=[("min", "min"), ("max", "max"), ("none", "none")], max_length=4)
     infection_minimum_lrv_min = models.FloatField()
     infection_minimum_lrv_max = models.FloatField()
     infection_minimum_lrv_q1 = models.FloatField()
@@ -358,7 +362,6 @@ class RiskAssessmentResult(models.Model):
     infection_maximum_lrv_q1 = models.FloatField()
     infection_maximum_lrv_q3 = models.FloatField()
     infection_maximum_lrv_median = models.FloatField()
-
     dalys_minimum_lrv_min = models.FloatField()
     dalys_minimum_lrv_max = models.FloatField()
     dalys_minimum_lrv_q1 = models.FloatField()
@@ -369,3 +372,31 @@ class RiskAssessmentResult(models.Model):
     dalys_maximum_lrv_q1 = models.FloatField()
     dalys_maximum_lrv_q3 = models.FloatField()
     dalys_maximum_lrv_median = models.FloatField()
+
+    def as_dict(self):
+        return dict(
+            ra_name=self.risk_assessment.name,
+            pathogen=self.pathogen,
+            infection_risk=self.infection_risk,
+            dalys_risk=self.dalys_risk,
+            infection_minimum_lrv_min=self.infection_minimum_lrv_min,
+            infection_minimum_lrv_max=self.infection_minimum_lrv_max,
+            infection_minimum_lrv_q1=self.infection_minimum_lrv_q1,
+            infection_minimum_lrv_q3=self.infection_minimum_lrv_q3,
+            infection_minimum_lrv_median=self.infection_minimum_lrv_median,
+            infection_maximum_lrv_min=self.infection_maximum_lrv_min,
+            infection_maximum_lrv_max=self.infection_maximum_lrv_max,
+            infection_maximum_lrv_q1=self.infection_maximum_lrv_q1,
+            infection_maximum_lrv_q3=self.infection_maximum_lrv_q3,
+            infection_maximum_lrv_median=self.infection_maximum_lrv_median,
+            dalys_minimum_lrv_min=self.dalys_minimum_lrv_min,
+            dalys_minimum_lrv_max=self.dalys_minimum_lrv_max,
+            dalys_minimum_lrv_q1=self.dalys_minimum_lrv_q1,
+            dalys_minimum_lrv_q3=self.dalys_minimum_lrv_q3,
+            dalys_minimum_lrv_median=self.dalys_minimum_lrv_median,
+            dalys_maximum_lrv_min=self.dalys_maximum_lrv_min,
+            dalys_maximum_lrv_max=self.dalys_maximum_lrv_max,
+            dalys_maximum_lrv_q1=self.dalys_maximum_lrv_q1,
+            dalys_maximum_lrv_q3=self.dalys_maximum_lrv_q3,
+            dalys_maximum_lrv_median=self.dalys_maximum_lrv_median
+        )