fixes from user testing feedbacks

adaurat · adaurat · commit 190dc31a35bd · 2025-07-23T15:57:23.000+02:00
diff --git a/infra/helm/qmra/dev.values.yaml b/infra/helm/qmra/dev.values.yaml
@@ -6,6 +6,7 @@ namespace: qmra
 domain: dev.qmra.org
 monitoring_domain: dev2.qmra.org
 replicaCount: 1
+debug: true
 
 app_secret_key:
   secret_name: qmra-secret-key-secret
diff --git a/infra/helm/qmra/prod.values.yaml b/infra/helm/qmra/prod.values.yaml
@@ -6,6 +6,7 @@ namespace: qmra
 domain: qmra.org
 monitoring_domain: monitoring.qmra.org
 replicaCount: 1
+debug: false
 
 app_secret_key:
   secret_name: qmra-secret-key-secret
diff --git a/infra/helm/qmra/templates/configmap.yaml b/infra/helm/qmra/templates/configmap.yaml
@@ -4,7 +4,7 @@ metadata:
   namespace: {{ .Values.namespace }}
   name: {{ .Values.configmap_name }}
 data:
-  DEBUG: "true"
+  DEBUG: {{ .values.debug }}
   DOMAIN_NAME: {{ .Values.domain }}
   SQLITE_PATH: {{ .Values.sqlite.mount_path }}
   STATIC_ROOT: {{ .Values.static.mount_path }}
diff --git a/qmra/risk_assessment/plots.py b/qmra/risk_assessment/plots.py
@@ -31,7 +31,8 @@ def risk_plots(risk_assessment_results, output_type="div"):
             q3=[r.infection_minimum_lrv_q3, r.infection_maximum_lrv_q3],
             median=[r.infection_minimum_lrv_median, r.infection_maximum_lrv_median],
             name=r.pathogen,
-            marker=dict(color=COLORS[r.pathogen])
+            marker=dict(color=COLORS[r.pathogen]),
+            hoverinfo="y"
         ))
         # 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(
@@ -42,7 +43,8 @@ def risk_plots(risk_assessment_results, output_type="div"):
             q3=[r.dalys_minimum_lrv_q3, r.dalys_maximum_lrv_q3],
             median=[r.dalys_minimum_lrv_median, r.dalys_maximum_lrv_median],
             name=r.pathogen,
-            marker=dict(color=COLORS[r.pathogen])
+            marker=dict(color=COLORS[r.pathogen]),
+            hoverinfo="y"
         ))
         # dalys_fig.add_annotation(text=r.pathogen, showarrow=False, xref="paper", yref="paper", x=(i+1)/7, y=0)
 
@@ -73,9 +75,9 @@ def risk_plots(risk_assessment_results, output_type="div"):
                                      text="tolerable risk level",
                                      textposition="end",
                                      yanchor="top",
-                                     font=dict(color="#FFAA27")
+                                     font=dict(color="#FF0000")
                                  ),
-                                 line=dict(color="#FFAA27", width=3)
+                                 line=dict(color="#FF0000", width=1)
                                  )
     infection_prob_fig.update_traces(
         marker_size=8
@@ -107,14 +109,24 @@ def risk_plots(risk_assessment_results, output_type="div"):
                             text="tolerable risk level",
                             textposition="end",
                             yanchor="top",
-                            font=dict(color="#FFAA27")
+                            font=dict(color="#FF0000")
                         ),
-                        line=dict(color="#FFAA27", width=3)
+                        line=dict(color="#FF0000", width=1)
                         )
     dalys_fig.update_traces(
         marker_size=8
     )
     if output_type == "div":
-        return plot(infection_prob_fig, output_type="div", config={"displaylogo": False, "modeBarButtonsToRemove": ['zoom2d', 'pan2d', 'select2d', 'lasso2d', 'zoomIn2d', 'zoomOut2d', 'autoScale2d', 'resetScale2d']}, include_plotlyjs=False), \
-            plot(dalys_fig, output_type="div", config={"displaylogo": False, "modeBarButtonsToRemove": ['zoom2d', 'pan2d', 'select2d', 'lasso2d', 'zoomIn2d', 'zoomOut2d', 'autoScale2d', 'resetScale2d']}, include_plotlyjs=False)
+        return plot(infection_prob_fig, output_type="div", config={"displaylogo": False,
+                                                                   "modeBarButtonsToRemove": ['zoom2d', 'pan2d',
+                                                                                              'select2d', 'lasso2d',
+                                                                                              'zoomIn2d', 'zoomOut2d',
+                                                                                              'autoScale2d',
+                                                                                              'resetScale2d']},
+                    include_plotlyjs=False), \
+            plot(dalys_fig, output_type="div", config={"displaylogo": False,
+                                                       "modeBarButtonsToRemove": ['zoom2d', 'pan2d', 'select2d',
+                                                                                  'lasso2d', 'zoomIn2d', 'zoomOut2d',
+                                                                                  'autoScale2d', 'resetScale2d']},
+                 include_plotlyjs=False)
     return infection_prob_fig.to_image(format=output_type), dalys_fig.to_image(format=output_type)
diff --git a/qmra/risk_assessment/risk.py b/qmra/risk_assessment/risk.py
@@ -14,7 +14,8 @@ def get_annual_risk(
         n_events: int = 10_000,
         n_years: int = 1000,
 ):
-    inflow = np.random.normal(
+    generator = np.random.default_rng(seed=42)
+    inflow = generator.normal(
         loc=(np.log10(inflow_min + 10 ** (-8)) + np.log10(inflow_max)) / 2,
         scale=(np.log10(inflow_max) - np.log10(inflow_min + 10 ** (-8))) / 4,
         size=n_events
@@ -23,7 +24,7 @@ def get_annual_risk(
     outflow = inflow - lrv
     dose = (10 ** outflow) * volume_per_event
     event_probs = distribution.pdf(dose)
-    event_samples = np.random.choice(event_probs, size=(n_years, events_per_year), replace=True)
+    event_samples = generator.choice(event_probs, size=(n_years, events_per_year), replace=True)
     return 1 - np.prod(1 - event_samples, axis=1)
 
 
diff --git a/qmra/risk_assessment/templates/assessment-configurator.html b/qmra/risk_assessment/templates/assessment-configurator.html
@@ -85,7 +85,7 @@ <h4 class="ml-3">Risk assessment parameters</h4>
                     <h4>Exposure: <span id="exposure-info-name"></span></h4>
                     <div class="test-muted small mb-4" id="exposure-info-description"></div>
                     <div class="mb-4" id="exposure-info-values"></div>
-                    <div class="small mb-4"><sup>[1]</sup>values taken from <a id="exposure-info-reference" href=""></a>
+                    <div class="small mb-4"><sup>[1]</sup>values taken from <a id="exposure-info-reference" href="" target="_blank" rel="noopener noreferrer"></a>
                     </div>
                 </div>
                 <div id="source-info">
@@ -115,7 +115,7 @@ <h4>Source water: <span id="source-info-name"></span></h4>
                             </tr>
                         </table>
                     </div>
-                    <div class="small mb-4"><sup>[1]</sup>values taken from <a id="source-info-reference" href=""></a>
+                    <div class="small mb-4"><sup>[1]</sup>values taken from <a id="source-info-reference" href="" target="_blank" rel="noopener noreferrer"></a>
                     </div>
                 </div>
                 <div id="treatment-info">
@@ -156,6 +156,8 @@ <h4>Treatments</h4>
                 e.preventDefault();
                 e.stopPropagation();
                 if (!form.checkValidity()) { form.reportValidity(); return; }
+                const accepted_redirect = confirm("Any unsaved changes to your risk assessment will be lost.\nAre you sure you want to continue?")
+                if (!accepted_redirect) return;
                 const frm = new FormData(form);
                 return fetch(form.action, {
                     method: "POST",
diff --git a/qmra/risk_assessment/templates/assessment-result.html b/qmra/risk_assessment/templates/assessment-result.html
@@ -40,7 +40,7 @@ <h4 class="mt-3 mx-5 text-center">Result</h4>
         <br/>
         <div>
             <strong>More efficient treatments or additional treatment
-                steps are necessary to achieve a tolerable risk level for the water reuse scenario.
+                steps are likely to be necessary to achieve a tolerable risk level for the water reuse scenario.
             </strong>
         </div>
         {% endif %}
diff --git a/qmra/risk_assessment/templates/configurator-guided-tour.html b/qmra/risk_assessment/templates/configurator-guided-tour.html
@@ -20,7 +20,7 @@
         },
         {
             title: "Step 4: Treatment",
-            content: "Finally, select the treatment processes that have been planned or are currently implemented in your system to complete your risk assessment. Each treatment option is associated with a specific Log Removal Value (LRV) for viruses, bacteria, and protozoan parasites. The QMRA tool includes a range of default LRVs derived from international guidance documents for both wastewater and drinking water technologies. For the most accurate results, consider using locally obtained removal values. The tool is highly customizable, allowing you to add your own treatments by clicking on “My Treatments” in the navigation bar, include non-technical barriers (e.g. hygiene practices), or even apply a negative LRV to simulate recontamination scenarios.",
+            content: "Finally, select the treatment processes that have been planned or are currently implemented in your system to complete your risk assessment. Each treatment option is associated with a specific Log Removal Value (LRV) for viruses, bacteria, and protozoan parasites. LRVs are determined by measuring pathogens (or indicator organisms) in the influent and effluent of the treatment step and calculating LRV by: <math display='block'><mrow><mi>LRV</mi><mo>=</mo><msub><mi>log</mi><mn>10</mn></msub><mfrac><mrow><mi>influent concentration</mi></mrow><mrow><mi>effluent concentration</mi></mrow></mrow></math> The QMRA tool includes a range of default LRVs derived from international guidance documents for both wastewater and drinking water technologies. For the most accurate results, consider using locally obtained removal values. The tool is highly customizable, allowing you to add your own treatments in the “New Treatment” tab on the right of the risk assessment configuration page, include non-technical barriers (e.g. hygiene practices), or even apply a negative LRV to simulate recontamination scenarios. Note: Click the “Save & Continue” Button and save your risk assessment before creating a new treatment.",
             target: "#treatment-content",
             order: 3
         },
diff --git a/qmra/risk_assessment/templates/faqs.html b/qmra/risk_assessment/templates/faqs.html
@@ -9,9 +9,7 @@ <h5>1. What is Quantitative Microbial Risk Assessment (QMRA)?</h5>
         to assess the likelihood of illness from pathogens in water.</p>
     <h5>2. Is this tool free to use?</h5>
     <p>Yes, the QMRA tool is completely free to use. It provides you with powerful resources and guidance to assess
-        microbial risks in your water reuse schemes without any cost. You can access the underlying database here (link
-        to
-        Aquanes database) and associated <a href="https://github.com/KWB-R/qmra-webapp">github repository</a>.</p>
+        microbial risks in your water reuse schemes without any cost.</p>
     <h5>3. Who should use this QMRA tool?</h5>
     <p>This tool is designed for water safety professionals, engineers, and public health officials involved in water
         reuse schemes. It is also suitable for researchers, students, and anyone interested in understanding the risks
@@ -87,7 +85,7 @@ <h5>6. What types of water reuse schemes can this tool assess?</h5>
     <h5>7. What data are used in the tool and where can I access them?</h5>
     <p>The tool uses data (e.g. pathogen concentrations in different source waters, LRV for specific water treatments)
     derived from scientific literature and international guidance documents. All references are transparently listed in
-    the “Reference” tab of the risk assessment configuration page, and in the QMRA tool database (Link to the database).</p>
+    the “Reference” tab of the risk assessment configuration page.</p>
     <h5>8. Can I customize the parameters in the tool?</h5>
     <p>Absolutely! While the tool provides default values and guidance, you can fully customize the parameters, such as
     pathogen concentrations, treatment effectiveness (Log Removal Values - LRV), and exposure scenarios, to match your
@@ -108,8 +106,8 @@ <h5>11. What support is available if I have questions?</h5>
     documentation or contact our support team for assistance.</p>
     <h5>12. Is the tool compliant with international guidelines?</h5>
     <p>Yes, the tool is developed based on international guidelines for water safety and QMRA, ensuring that your
-    assessments are aligned with best practices and standards. The specific guidelines used are accessible via the QMRA
-    database (Link to database).</p>
+    assessments are aligned with best practices and standards. The specific guidelines used are accessible via the "Reference"
+        tab of the risk assessment configuration page.</p>
     <h5>13. What are the limitations of this tool?</h5>
     <p>While the QMRA Tool is a powerful resource for assessing microbial risks in water reuse schemes, it does have some
     limitations:</p>
diff --git a/qmra/risk_assessment/templates/risk-assessment-list.html b/qmra/risk_assessment/templates/risk-assessment-list.html
@@ -4,6 +4,8 @@
 <script type="text/javascript">
     const baseUrl = '/assessment'
     function deleteAssessment(assessmentId) {
+        const confirmed = confirm("Are you sure that you want to delete this assessment?")
+        if (!confirmed) return;
         fetch(baseUrl + '/' + assessmentId, {
             method: "DELETE",
             headers: { 'X-CSRFToken': document.querySelector('[name=csrfmiddlewaretoken]').value },
@@ -97,7 +99,8 @@ <h4 class="media-heading text-truncate kwb_headline">
             <a data-toggle="tooltip" title="edit" class="mr-1" href="{% url 'assessment' assessment.id %}">
                 <img src="{% static 'img/pen.svg' %}">
             </a>
-            <label data-toggle="tooltip" title="delete" onclick="event.stopPropagation(); deleteAssessment('{{assessment.id}}')" style="cursor: pointer;">
+            <label data-toggle="tooltip" title="delete"
+                   onclick="event.preventDefault(); deleteAssessment('{{assessment.id}}')" style="cursor: pointer;">
                 <input type="submit" hidden="hidden">
 
                 <img src="{% static 'img/close.svg' %}">
@@ -135,7 +138,7 @@ <h4 class="media-heading text-truncate kwb_headline">
                 <h5>Welcome to the QMRA Tool for Water Reuse</h5>
                 <p>This tool is designed to support Quantitative Microbial Risk Assessment (QMRA) for human health in the
                 context of water reuse. Whether you're evaluating the safety of treated wastewater or other reclaimed
-                    water sources, this tool helps you assess potential health risks associated with microbial contaminants.</p>
+                    water sources, this tool helps you toassess potential health risks associated with microbial contaminants.</p>
                 <h5>Free and User-Friendly</h5>
                 <p>Our QMRA tool is completely free to use, offering you a powerful resource to assess microbial risks in
                     water reuse schemes. You can use the tool without logging in, making it quick and easy to get started.</p>
@@ -196,22 +199,23 @@ <h5>Enhanced Features for Registered Users</h5>
                 },
                 shapes: [{
                     type: 'line',
-                    label: {text: "tolerable risk level", font: {color: '#FFAA27', size: 14}, textposition: "end"},
+                    label: {text: "tolerable risk level", font: {color: '#FF0000', size: 14}, textposition: "end"},
                     x0: 0,
                     y0: .0001,
                     x1: 1,
                     y1: .0001,
                     xref: "paper",
                     line: {
-                        color: '#FFAA27',
-                        width: 2,
+                        color: '#FF0000',
+                        width: 1,
                         dash: 'dashdot'
                     }
                 }],
                 xaxis: {
                     autorange: true,
-                    automargin: true
-                },
+                    automargin: true,
+                    tickfont: {size: 16}
+                    },
                 autosize: true,
                 font_color: "black",
                 margin: { t: 0 },
@@ -253,7 +257,6 @@ <h5>Enhanced Features for Registered Users</h5>
             xaxis: "x",
             yaxis: "y",
             marker: { color: color, opacity: .75, fillmode: "overlay", pattern: {shape: "/"} },
-
             showlegend: i === 0,
             offsetgroup: r.pathogen,
             legendgroup: "min - max range",
diff --git a/qmra/risk_assessment/templates/treatments-form-js.html b/qmra/risk_assessment/templates/treatments-form-js.html
diff --git a/qmra/settings.py b/qmra/settings.py
diff --git a/qmra/templates/index.html b/qmra/templates/index.html
diff --git a/test.zip b/test.zip

Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,7 @@`
`20`	`20`	`},`
`21`	`21`	`{`
`22`	`22`	`title: "Step 4: Treatment",`
`23`		- content: "Finally, select the treatment processes that have been planned or are currently implemented in your system to complete your risk assessment. Each treatment option is associated with a specific Log Removal Value (LRV) for viruses, bacteria, and protozoan parasites. The QMRA tool includes a range of default LRVs derived from international guidance documents for both wastewater and drinking water technologies. For the most accurate results, consider using locally obtained removal values. The tool is highly customizable, allowing you to add your own treatments by clicking on “My Treatments” in the navigation bar, include non-technical barriers (e.g. hygiene practices), or even apply a negative LRV to simulate recontamination scenarios.",
	`23`	+ content: "Finally, select the treatment processes that have been planned or are currently implemented in your system to complete your risk assessment. Each treatment option is associated with a specific Log Removal Value (LRV) for viruses, bacteria, and protozoan parasites. LRVs are determined by measuring pathogens (or indicator organisms) in the influent and effluent of the treatment step and calculating LRV by: <math display='block'><mrow><mi>LRV</mi><mo>=</mo><msub><mi>log</mi><mn>10</mn></msub><mfrac><mrow><mi>influent concentration</mi></mrow><mrow><mi>effluent concentration</mi></mrow></mrow></math> The QMRA tool includes a range of default LRVs derived from international guidance documents for both wastewater and drinking water technologies. For the most accurate results, consider using locally obtained removal values. The tool is highly customizable, allowing you to add your own treatments in the “New Treatment” tab on the right of the risk assessment configuration page, include non-technical barriers (e.g. hygiene practices), or even apply a negative LRV to simulate recontamination scenarios. Note: Click the “Save & Continue” Button and save your risk assessment before creating a new treatment.",
`24`	`24`	`target: "#treatment-content",`
`25`	`25`	`order: 3`
`26`	`26`	`},`